-
-
+
-Build GAMBLR
-
-Build GAMBLR
-
If you are viewing this page on Github, consider clicking this link to go to the GAMBLR webpage and learn more about this package.
If you have access to gphost, the easiest way to obtain and run GAMBLR is to do this via Rstudio on a gphost. If you do not have access to gphost, please refer to the Run Remote On A Local Machine section. Assuming you are running Rstudio on gphost, clone the repo to your home directory (not your GAMBL working directory).
git clone git@github.com:morinlab/GAMBLR.gitIn Rstudio (on a gphost), set your working directory to the place you just cloned the repo.
-setwd("~/GAMBLR")setwd("~/GAMBLR-master")Install the package in R by running the following command (requires the devtools package)
devtools::install()If you don’t have access to gphost on GSC, no worries, you can still execute GAMBLR functions in another way. Remote support was developed for this purpose. This section explains how to run GAMBLR remote on a local machine. There are two different approaches to get this to work, both with its own advantages and limitations. We will be going over both in this next section.
-This section details how to deploy GAMBLR with limited functionality, using ssh_session parameter. This approach requires either a working GSC VPN connection (or is directly accessible if connected to the GSC network).
+If you don’t have access to gphost on GSC, no worries, you can still execute GAMBLR functions in another way. Remote support was developed for this purpose. This section explains how to run GAMBLR remote on a local machine (i.e on your own computer). There are two different approaches to get this to work, both with its own advantages and limitations. We will be going over both in this next section.
+This section details how to deploy GAMBLR with limited functionality. This approach requires either a working GSC VPN connection (or is directly accessible if connected to the GSC network).
remote:
project_base: "/path/to/your/local/gambl_results_directory/"
@@ -214,30 +212,24 @@ Clone Repos, Update Paths, Install and Load R Packages
setwd("~/git_repos/GAMBLR-master")devtools::install()
-install.packages("ssh")devtools::install()library(GAMBLR)
-library(ssh)library(GAMBLR)session = GAMBLR::get_ssh_session()Sys.setenv(R_CONFIG_ACTIVE = "remote")get_gambl_metadata() to retrieve meta data for all gambl samples).get_gambl_metadata() %>%
diff --git a/README.md b/README.md
index c2dad948..bb52e696 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# 
+#
# GABMLR - an R package with convenience functions for working with GAMBL results.
@@ -202,17 +202,17 @@ Error: '/projects/rmorin/projects/gambl-repos/gambl-rmorin/data/metadata/gambl_a
## Contributing
As GAMBL users (GAMBLRs, so to speak) rely on the functionality of this package, the Master branch is protected. All commits must be submitted via pull request on a branch. Please refer to the [GAMBL](https://github.com/morinlab/gambl#contribution-guidelines) documentation for details on how to do this.
-### For Developers
-When designing new functions, please refer to guid-lines and best practices detailed [here](https://r-pkgs.org/). For your convenience, here is an empty function-skeleton that can be recycled when designing new GAMBLR functions. Ensure to always provide the required documentation for any new functions. See [this](https://r-pkgs.org/man.html#title-description-details) section for more details on best practices for documenting R functions. Unsure what information goes where in a function documentation? Here is a brief outline for what the different sections should include. For more information, see [this](https://r-pkgs.org/man.html#title).
+### New Functions
+When designing new functions, please refer to guide-lines and best practices detailed [here](https://r-pkgs.org/). Ensure to always provide the required documentation for any new functions. See [this](https://r-pkgs.org/man.html#title-description-details) section for more details on best practices for documenting R functions. Unsure what information goes where in a function documentation? Here is a brief outline for what the different sections should include and as an example, [here](https://github.com/morinlab/GAMBLR/blob/master/R/viz.R#L2423) is an adequately documented GAMBLR function. For more information, see [this](https://r-pkgs.org/man.html#title).
#### Title
-The title is taken from the first sentence. It should be written in sentence case, not end in a full stop, and be followed by a blank line. The title is shown in various function indexes (e.g. help(package = "somepackage")) and is what the user will usually see when browsing multiple functions.
+The title is taken from the first sentence. It should be written in sentence case, not end in a full stop, and be followed by a blank line. The title is shown in various function indexes (e.g. help(package = "some_package")) and is what the user will usually see when browsing multiple functions.
#### Description
The description is taken from the next paragraph. It’s shown at the top of documentation and should briefly describe the most important features of the function.
#### Details
-Additional details are anything after the description. Details are optional, but can be any length so are useful if you want to dig deep into some important aspect of the function. Note that, even though the details come right after the description in the introduction, they appear much later in rendered documentation.
+Additional details are anything after the description. Details are optional, but can be any length so are useful if you want to dig deep into some important aspect of the function. Note that, even though the details come right after the description in the introduction, they appear much later in rendered documentation. If you want to add code in any other language other than R, this is also the sections to do so. For example, the new function relies on some bash code in order to utilize the GAMBLR code. You can detail such code here by simply adding a code block as you would in a regular markdown file.
#### Parameters
Detailed parameter descriptions should be included for all functions. Remember to state the required data types, default values, if the parameter is required or optional, etc.
@@ -221,14 +221,33 @@ Detailed parameter descriptions should be included for all functions. Remember t
Specify the returned object, is it a data frame, a list, a vector or characters, etc.
#### Import
-Always import all the packages from which you are calling any functions outside of base R and R [packages](https://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Add_002dOn-Packages) that gets loaded per default. Remember to not import `tidyverse`, rather, import the individual packages from `tidyverse` that the function is depending on.
+Always import all the packages from which you are calling any functions outside of base R and R [packages](https://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Add_002dOn-Packages) that gets loaded per default. Remember to not import `tidyverse`, rather, import the individual packages from `tidyverse` that the function is depending on. If any packages that are not yet a part of the GAMBLR dependencies are needed for the function, the user needs to run `usethis::use_package("package_name")` in order to add any such new dependencies to DESCRIPTION. Warning, do not edit DESCRIPTION by hand, instead use the approach detailed here.
#### Export
-Should this function be exported to NAMESPACE (i.e make it directly accessible for anyone who loads GAMBLR) or is the function considered to be an internal/helper function (i.e don't export it)?
+Should this function be exported to NAMESPACE (i.e make it directly accessible for anyone who loads GAMBLR), or is the function considered to be an internal/helper function? In order to have the function populate NAMESPACE, the developer has to run `devtools::document()`. All functions that have the `@export` line in its documentation will be added to NAMESPACE. Helper functions should not include this in the function documentation. Note that such functions are still accessible with `GAMBLR:::helper_function_name`. If The new function is indeed a helper/internal function, ensure that this is made clear from both the function description and details (see [this](https://github.com/morinlab/GAMBLR/blob/master/R/utilities.R#L785) example). In addition, it should also be clear what purpose the helper function is serving (i.e what other GAMBLR functions are calling the helper function).
#### Examples
-Please provide fully reproducible examples for the function. Ideally, the example should demonstrate basic usage, as well as more advanced usage with different parameter combinations. Note that examples can not extend over 100 characters per line, since this will cause the lines to be truncated in the rendered PDF manual.
+Please provide fully reproducible examples for the function. Ideally, the example should demonstrate basic usage, as well as more advanced usage with different parameter combinations. Note that examples can not extend over 100 characters per line, since this will cause the lines to be truncated in the rendered PDF manual. In addition, the developer needs to load any packages (besides **GAMBLR**) that are needed to run the examples. For instance, if the example code calls `%>%`, `dplyr` or `magrittr` to make the pipe available for the example. It is advised to write your example in such a way that loading external packages are avoided as much as possible. Instead, prioritize base R as much as possible. In some cases, it is undesirable to have a function run its examples. This applies to functions that are writing files and helper functions. To avoid any such examples to run, simply wrap the example in:
+```
+\dontrun{
+do_not_run = some_function()
+}
+```
+
+#### Helper Function Specific Instructions
+If the newly added function is a utilized by GAMBLR as an internal or helper function, you should also add the `@noRd` field to the function documentation. This prevents the function to have an `.Rd` file created and populated in the `man/` folder. This is important, since such functions should not be represented on the website that is being built from the source code. In addition, make sure that you also followed the helper function specific instructions under **Examples** and **Export**.
+
+### Testing New Functions
+So you have added a new function (carefully following the steps in the previous section!) and you are obviously extremely proud and eager to test it out (and let others test it). There are basically two different approaches to do so.
+
+#### Option 1
+Your first option, and likely the preferred route to take, is to make sure that the working directory in R studio is set to the GAMBLR folder with your updated code and then run `devtools::load_all()` to load all the functions available in the `R/` folder of thee same repo. This should make all such functions available to call.
+
+#### Option 2
+As an alternative, you can also run `devtools::install()` from the updated GAMBLR directory. As the name implies, this will install the complete package complete with dependencies, remotes, etc. **Note**, if you run with the second option, make sure to restart your R session with `.rs.restartR()` after installing the package and then load GAMBLR with `library(GAMBLR)`. Now you have installed the updated branch of GAMBLR and are free to call any functions available in the `R/`
+### Function Documentation Template
+For your convenience, here is a documentation template for GAMBLR functions.
```
#' @title
#'
@@ -248,59 +267,7 @@ Please provide fully reproducible examples for the function. Ideally, the exampl
#' #this is an example
#' ###For your reference, this line is exactly 100 characters. Do not exceed 100 characters per line
#'
-
function_name = function(a_parameter,
another_parameter){
}
```
-#### Example Function
-For your convenience, as an example, here is a perfectly documented GAMBLR function, following the best practices detailed above.
-
-```
-#' @title ASHM Rainbow Plot
-#'
-#' @description Make a rainbow plot of all mutations in a region, ordered and coloured by metadata.
-#'
-#' @details This function creates a rainbow plot for all mutations in a region. Region can either be specified with the `region` parameter,
-#' or the user can provide a maf that has already been subset to the region(s) of interest with `mutation_maf`.
-#' As a third alternative, the regions can also be specified as a bed file with `bed`.
-#' Lastly, this function has a variety of parameters that can be used to further customize the returned plot in many different ways.
-#' Refer to the parameter descriptions, examples as well as the vignettes for more demonstrations how this function can be called.
-#'
-#' @param mutations_maf A data frame containing mutations (MAF format) within a region of interest (i.e. use the get_ssm_by_region).
-#' @param metadata should be a data frame with sample_id as a column.
-#' @param exclude_classifications Optional argument for excluding specific classifications from a metadeta file.
-#' @param drop_unmutated Boolean argument for removing unmutated sample ids in mutated cases.
-#' @param classification_column The name of the metadata column to use for ordering and colouring samples.
-#' @param bed Optional data frame specifying the regions to annotate (required columns: start, end, name).
-#' @param region Genomic region for plotting in bed format.
-#' @param custom_colours Provide named vector (or named list of vectors) containing custom annotation colours if you do not want to use standartized pallette.
-#' @param hide_ids Boolean argument, if TRUE, ids will be removed.
-#'
-#' @return ggplot2 object.
-#'
-#' @import dplyr ggplot2
-#' @export
-#'
-#' @examples
-#' #basic usage
-#' region = "chr6:90975034-91066134"
-#' metadata = get_gambl_metadata()
-#' plot = ashm_rainbow_plot(metadata = metadata, region = region)
-#'
-#' #advanced usages
-#' mybed = data.frame(start = c(128806578,
-#' 128805652,
-#' 128748315),
-#' end = c(128806992,
-#' 128809822,
-#' 128748880),
-#' name = c("TSS",
-#' "enhancer",
-#' "MYC-e1"))
-#'
-#' ashm_rainbow_plot(mutations_maf = my_mutations,
-#' metadata = my_metadata,
-#' bed = mybed)
-#'
-```
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 01314c00..a34b2fdb 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -14,6 +14,7 @@ home:
href: https://github.com/morinlab/GAMBLR/issues
- text: Insights
href: https://github.com/morinlab/GAMBLR/pulse
+search:
reference:
- title: Annotations
desc: Functions used to annotate GAMBL data.
diff --git a/config.yml b/config.yml
index c080f27b..6e80f10f 100644
--- a/config.yml
+++ b/config.yml
@@ -22,6 +22,9 @@ default:
augmented: "all_the_things/slms_3-1.0_vcf2maf-1.3/{seq_type}--projection/deblacklisted/augmented_maf/all_slms-3--{projection}.CDS.maf"
cnv: "all_the_things/cnv_master-1.0/merges/{seq_type}--{projection}.seg"
sv: "all_the_things/svar_master-1.0/merges/gridss_manta.genome--{projection}.bedpe"
+ manta_sv:
+ gambl: "gambl/manta-2.3/merges/manta.genome--{projection}.bedpe"
+ icgc_dart: "all_the_things/manta-2.3/merges/manta.genome--{projection}.bedpe"
results_merged_wildcards:
lymphgen_template: "no_cnvs.no_sv.with_A53,no_cnvs.no_sv.no_A53,no_cnvs.with_sv.with_A53,with_cnvs.no_sv.no_A53,no_cnvs.with_sv.no_A53,with_cnvs.no_sv.with_A53,with_cnvs.with_sv.no_A53,with_cnvs.with_sv.with_A53"
results_versioned:
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diff --git a/docs/articles/function_index.html b/docs/articles/function_index.html
new file mode 100644
index 00000000..daf7866a
--- /dev/null
+++ b/docs/articles/function_index.html
@@ -0,0 +1,186 @@
+
+
+
+
+
+
+
+Function Index • GAMBLR
+
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+
+ Function Index
+
+
+
+ function_index.Rmd
+
+
+
+
+
+
+Where can I find the source code for any given GAMBLR function?
+
+Ever wondered where a specific function lives in the source code, or how any given function is being classified? For your convenience, here is a complete table with all currently available GAMBLR functions. Note that helper functions are not included in this list, since such functions are not exported to NAMESPACE. In addition, the bundled data sets are also not included.
+
+
+
+
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index 510c8d95..0f615e7a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -74,6 +74,13 @@
Functions & Bundled Data
+-
+
+
+
+ Function Index
+
+
-
@@ -101,6 +108,8 @@
All vignettes
-
- Fancy Plots Tutorial
-
+
- Function Index
+ -
- SSM Tutorial
-
- Utilities Tutorial
diff --git a/docs/articles/ssm_tutorial.html b/docs/articles/ssm_tutorial.html
index 8146226d..c02fcecb 100644
--- a/docs/articles/ssm_tutorial.html
+++ b/docs/articles/ssm_tutorial.html
@@ -423,320 +423,15 @@ Rainbow Plots= fl_dlbcl_metadata,
classification_column = "pathology",
seq_type = "genome",
+ verbose = FALSE,
regions_to_display = c("BCL2-TSS", "MYC-TSS"))
## chr_name hg19_start hg19_end gene region
-## 1 chr1 6661482 6662702 KLHL21 TSS
-## 2 chr1 23885584 23885835 ID3 TSS
-## 3 chr1 150550814 150552135 MCL1 intronic
-## 4 chr1 203274698 203275778 BTG2 intronic
-## 5 chr1 226864857 226873452 ITPKB intronic
-## 6 chr1 226920563 226927885 ITPKB TSS
-## 7 chr1 226921088 226927982 ITPKB intron-1
-## 8 chr2 60773789 60783486 BCL11A TSS
-## 9 chr2 96808901 96811913 DUSP2 intron-1
-## 10 chr2 111874854 111882174 BCL2L11 TSS
-## 11 chr2 136874728 136875461 CXCR4 intronic
-## 12 chr3 16546433 16556786 RFTN1 TSS
-## 13 chr3 32020518 32024930 OSBPL10 TSS-1
-## 14 chr3 71104986 71119518 FOXP1 TSS-4
-## 15 chr3 71176427 71180960 FOXP1 TSS-3
-## 16 chr3 71350633 71357665 FOXP1 TSS-2
-## 17 chr3 71503103 71504870 FOXP1 intron-1b
-## 18 chr3 71550753 71551478 FOXP1 intron-1a
-## 19 chr3 71626341 71635648 FOXP1 TSS-1
-## 20 chr3 101546669 101547704 NFKBIZ TSS-1
-## 21 chr3 101568239 101569274 NFKBIZ TSS-2
-## 22 chr3 183269360 183274139 KLHL6 TSS
-## 23 chr3 186739628 186740875 ST6GAL1 TSS-1
-## 24 chr3 186782522 186784438 ST6GAL1 intronic-1
-## 25 chr3 187458526 187464632 BCL6 TSS
-## 26 chr3 187771678 187801626 LPP TSS-1
-## 27 chr3 187801627 187813568 LPP TSS-2
-## 28 chr3 187813569 187955254 LPP TSS-3
-## 29 chr3 187955255 187969220 LPP TSS-4
-## 30 chr3 188377178 188401951 LPP intronic-1
-## 31 chr3 188401952 188461879 LPP intronic-2
-## 32 chr3 188461880 188474683 LPP intronic-3
-## 33 chr3 188474684 188491248 LPP intronic-4
-## 34 chr4 40193105 40204231 RHOH TSS
-## 35 chr5 88131209 88174373 MEF2C TSS-3
-## 36 chr5 88174374 88182243 MEF2C TSS-2
-## 37 chr5 88182244 88206620 MEF2C TSS-1
-## 38 chr5 131823933 131826458 IRF1 TSS
-## 39 chr5 149790977 149792349 CD74 TSS
-## 40 chr5 158500476 158532769 EBF1 TSS
-## 41 chr6 390572 394093 IRF4 TSS
-## 42 chr6 14118026 14120025 CD83 TSS
-## 43 chr6 31548325 31550717 LTB intron-1
-## 44 chr6 37138104 37139804 PIM1 TSS
-## 45 chr6 90981034 91016134 BACH2 TSS
-## 46 chr6 134487960 134499859 SGK1 TSS-1
-## 47 chr6 159237903 159240216 EZR TSS
-## 48 chr7 5568297 5570856 ACTB TSS
-## 49 chr8 11347723 11355318 BLK TSS
-## 50 chr8 128748352 128749427 MYC TSS
-## 51 chr9 37023396 37027663 PAX5 intron-1
-## 52 chr9 37029849 37037154 PAX5 TSS-1
-## 53 chr9 37192080 37207549 ZCCHC7 intron-4
-## 54 chr9 37275952 37306152 ZCCHC7 intron-2
-## 55 chr9 37312655 37328260 ZCCHC7 intron-3
-## 56 chr9 37329706 37340398 ZCCHC7 intron-1
-## 57 chr9 37369209 37372160 PAX5 distal-enhancer-1
-## 58 chr9 37382267 37385854 PAX5 distal-enhancer-2
-## 59 chr9 37395932 37409239 PAX5 distal-enhancer-3
-## 60 chr9 37423010 37425279 GRHPR TSS
-## 61 chr10 127578912 127591133 FANK1 TSS
-## 62 chr11 9595246 9599502 WEE1 intronic
-## 63 chr11 35156769 35164248 CD44 TSS
-## 64 chr11 60223385 60225310 MS4A1 TSS
-## 65 chr11 65190369 65192380 NEAT1 ncRNA
-## 66 chr11 65265237 65268359 MALAT1 ncRNA
-## 67 chr11 102188170 102190077 BIRC3 TSS
-## 68 chr11 111248078 111250224 POU2AF1 TSS
-## 69 chr11 128339774 128345731 ETS1 introns
-## 70 chr11 128388492 128394163 ETS1 TSS-2
-## 71 chr12 11796001 11812968 ETV6 TSS
-## 72 chr12 25204045 25213569 LRMP TSS
-## 73 chr12 92537999 92539598 BTG1 TSS
-## 74 chr12 113492311 113497546 DTX1 TSS
-## 75 chr12 122456912 122464036 BCL7A TSS
-## 76 chr13 46957278 46963342 C13orf18 TSS
-## 77 chr14 69257848 69259739 ZFP36L1 TSS
-## 78 chr14 94940587 94942549 SERPINA9 TSS
-## 79 chr14 96179535 96180366 TCL1A TSS
-## 80 chr15 59658991 59671152 MYO1E TSS
-## 81 chr16 10970795 10975465 CIITA TSS
-## 82 chr16 11347512 11350007 SOCS1 intron-1
-## 83 chr16 27322895 27329423 IL4R TSS
-## 84 chr16 85931918 85933977 IRF8 TSS
-## 85 chr17 3597616 3599572 P2RX5 TSS
-## 86 chr17 56407732 56410140 TSPOAP1 intergenic
-## 87 chr17 75424734 75440956 SEPT9 intronic-1
-## 88 chr17 75443766 75451177 SEPT9 intronic-2
-## 89 chr17 75453203 75471471 SEPT9 intronic-3
-## 90 chr17 79478289 79479959 ACTG1 intronic
-## 91 chr18 60796984 60814103 BCL2 intronic
-## 92 chr18 60982728 60988342 BCL2 TSS
-## 93 chr19 10340142 10341764 S1PR2 TSS
-## 94 chr19 16434978 16439011 KLF2 TSS
-## 95 chr19 19279635 19281441 MEF2B TSS
-## 96 chr20 46128611 46138099 NCOA3 TSS
-## 97 chr20 49120482 49140477 PTPN1 TSS
-## 98 chr21 26934372 26937651 MIR155HG TSS
-## 99 chr22 23229554 23232042 IGLL5 TSS
-## 100 chrX 12993308 12994511 TMSB4X intronic
-## 101 chrX 48774756 48776255 PIM2 TSS
-## regulatory_comment regions
-## 1 <NA> chr1:6661482-6662702
-## 2 <NA> chr1:23885584-23885835
-## 3 <NA> chr1:150550814-150552135
-## 4 active_promoter chr1:203274698-203275778
-## 5 weak_enhancer chr1:226864857-226873452
-## 6 active_promoter chr1:226920563-226927885
-## 7 enhancer chr1:226921088-226927982
-## 8 active_promoter chr2:60773789-60783486
-## 9 enhancer chr2:96808901-96811913
-## 10 active_promoter chr2:111874854-111882174
-## 11 weak_promoter chr2:136874728-136875461
-## 12 active_promoter-strong_enhancer chr3:16546433-16556786
-## 13 active_promoter chr3:32020518-32024930
-## 14 active_promoter chr3:71104986-71119518
-## 15 active_promoter chr3:71176427-71180960
-## 16 active_promoter chr3:71350633-71357665
-## 17 intronic chr3:71503103-71504870
-## 18 intronic chr3:71550753-71551478
-## 19 active_promoter chr3:71626341-71635648
-## 20 active_promoter chr3:101546669-101547704
-## 21 active_promoter chr3:101568239-101569274
-## 22 active_promoter-strong_enhancer chr3:183269360-183274139
-## 23 active_promoter chr3:186739628-186740875
-## 24 strong_enhancer chr3:186782522-186784438
-## 25 <NA> chr3:187458526-187464632
-## 26 <NA> chr3:187771678-187801626
-## 27 <NA> chr3:187801627-187813568
-## 28 <NA> chr3:187813569-187955254
-## 29 <NA> chr3:187955255-187969220
-## 30 <NA> chr3:188377178-188401951
-## 31 <NA> chr3:188401952-188461879
-## 32 <NA> chr3:188461880-188474683
-## 33 <NA> chr3:188474684-188491248
-## 34 active_promoter chr4:40193105-40204231
-## 35 active_promoter chr5:88131209-88174373
-## 36 active_promoter chr5:88174374-88182243
-## 37 active_promoter chr5:88182244-88206620
-## 38 active_promoter chr5:131823933-131826458
-## 39 active_promoter chr5:149790977-149792349
-## 40 active_promoter chr5:158500476-158532769
-## 41 active_promoter chr6:390572-394093
-## 42 active_promoter-strong_enhancer chr6:14118026-14120025
-## 43 enhancer chr6:31548325-31550717
-## 44 active_promoter chr6:37138104-37139804
-## 45 <NA> chr6:90981034-91016134
-## 46 active_promoter chr6:134487960-134499859
-## 47 <NA> chr6:159237903-159240216
-## 48 active_promoter chr7:5568297-5570856
-## 49 strong_enhancer chr8:11347723-11355318
-## 50 active_promoter chr8:128748352-128749427
-## 51 intronic chr9:37023396-37027663
-## 52 active_promoter chr9:37029849-37037154
-## 53 intronic chr9:37192080-37207549
-## 54 intronic chr9:37275952-37306152
-## 55 intronic chr9:37312655-37328260
-## 56 intronic chr9:37329706-37340398
-## 57 enhancer chr9:37369209-37372160
-## 58 enhancer chr9:37382267-37385854
-## 59 enhancer chr9:37395932-37409239
-## 60 active_promoter chr9:37423010-37425279
-## 61 active_promoter chr10:127578912-127591133
-## 62 <NA> chr11:9595246-9599502
-## 63 active_promoter chr11:35156769-35164248
-## 64 active_promoter chr11:60223385-60225310
-## 65 enhancer chr11:65190369-65192380
-## 66 enhancer chr11:65265237-65268359
-## 67 active_promoter chr11:102188170-102190077
-## 68 active_promoter chr11:111248078-111250224
-## 69 enhancer chr11:128339774-128345731
-## 70 active_promoter chr11:128388492-128394163
-## 71 strong_enhancer chr12:11796001-11812968
-## 72 active_promoter chr12:25204045-25213569
-## 73 active_promoter chr12:92537999-92539598
-## 74 <NA> chr12:113492311-113497546
-## 75 poised_promoter chr12:122456912-122464036
-## 76 active_promoter chr13:46957278-46963342
-## 77 active_promoter chr14:69257848-69259739
-## 78 <NA> chr14:94940587-94942549
-## 79 active_promoter chr14:96179535-96180366
-## 80 <NA> chr15:59658991-59671152
-## 81 active_promoter-strong_enhancer chr16:10970795-10975465
-## 82 enhancer chr16:11347512-11350007
-## 83 active_promoter chr16:27322895-27329423
-## 84 active_promoter chr16:85931918-85933977
-## 85 active_promoter chr17:3597616-3599572
-## 86 enhancer chr17:56407732-56410140
-## 87 active_promoter chr17:75424734-75440956
-## 88 active_promoter chr17:75443766-75451177
-## 89 active_promoter chr17:75453203-75471471
-## 90 <NA> chr17:79478289-79479959
-## 91 strong_enhancer chr18:60796984-60814103
-## 92 active_promoter chr18:60982728-60988342
-## 93 active_promoter chr19:10340142-10341764
-## 94 intronic chr19:16434978-16439011
-## 95 active_promoter chr19:19279635-19281441
-## 96 active_promoter chr20:46128611-46138099
-## 97 active_promoter chr20:49120482-49140477
-## 98 active_promoter chr21:26934372-26937651
-## 99 <NA> chr22:23229554-23232042
-## 100 active_promoter chrX:12993308-12994511
-## 101 active_promoter chrX:48774756-48776255
-## name
-## 1 KLHL21-TSS
-## 2 ID3-TSS
-## 3 MCL1-intronic
-## 4 BTG2-intronic
-## 5 ITPKB-intronic
-## 6 ITPKB-TSS
-## 7 ITPKB-intron-1
-## 8 BCL11A-TSS
-## 9 DUSP2-intron-1
-## 10 BCL2L11-TSS
-## 11 CXCR4-intronic
-## 12 RFTN1-TSS
-## 13 OSBPL10-TSS-1
-## 14 FOXP1-TSS-4
-## 15 FOXP1-TSS-3
-## 16 FOXP1-TSS-2
-## 17 FOXP1-intron-1b
-## 18 FOXP1-intron-1a
-## 19 FOXP1-TSS-1
-## 20 NFKBIZ-TSS-1
-## 21 NFKBIZ-TSS-2
-## 22 KLHL6-TSS
-## 23 ST6GAL1-TSS-1
-## 24 ST6GAL1-intronic-1
-## 25 BCL6-TSS
-## 26 LPP-TSS-1
-## 27 LPP-TSS-2
-## 28 LPP-TSS-3
-## 29 LPP-TSS-4
-## 30 LPP-intronic-1
-## 31 LPP-intronic-2
-## 32 LPP-intronic-3
-## 33 LPP-intronic-4
-## 34 RHOH-TSS
-## 35 MEF2C-TSS-3
-## 36 MEF2C-TSS-2
-## 37 MEF2C-TSS-1
-## 38 IRF1-TSS
-## 39 CD74-TSS
-## 40 EBF1-TSS
-## 41 IRF4-TSS
-## 42 CD83-TSS
-## 43 LTB-intron-1
-## 44 PIM1-TSS
-## 45 BACH2-TSS
-## 46 SGK1-TSS-1
-## 47 EZR-TSS
-## 48 ACTB-TSS
-## 49 BLK-TSS
-## 50 MYC-TSS
-## 51 PAX5-intron-1
-## 52 PAX5-TSS-1
-## 53 ZCCHC7-intron-4
-## 54 ZCCHC7-intron-2
-## 55 ZCCHC7-intron-3
-## 56 ZCCHC7-intron-1
-## 57 PAX5-distal-enhancer-1
-## 58 PAX5-distal-enhancer-2
-## 59 PAX5-distal-enhancer-3
-## 60 GRHPR-TSS
-## 61 FANK1-TSS
-## 62 WEE1-intronic
-## 63 CD44-TSS
-## 64 MS4A1-TSS
-## 65 NEAT1-ncRNA
-## 66 MALAT1-ncRNA
-## 67 BIRC3-TSS
-## 68 POU2AF1-TSS
-## 69 ETS1-introns
-## 70 ETS1-TSS-2
-## 71 ETV6-TSS
-## 72 LRMP-TSS
-## 73 BTG1-TSS
-## 74 DTX1-TSS
-## 75 BCL7A-TSS
-## 76 C13orf18-TSS
-## 77 ZFP36L1-TSS
-## 78 SERPINA9-TSS
-## 79 TCL1A-TSS
-## 80 MYO1E-TSS
-## 81 CIITA-TSS
-## 82 SOCS1-intron-1
-## 83 IL4R-TSS
-## 84 IRF8-TSS
-## 85 P2RX5-TSS
-## 86 TSPOAP1-intergenic
-## 87 SEPT9-intronic-1
-## 88 SEPT9-intronic-2
-## 89 SEPT9-intronic-3
-## 90 ACTG1-intronic
-## 91 BCL2-intronic
-## 92 BCL2-TSS
-## 93 S1PR2-TSS
-## 94 KLF2-TSS
-## 95 MEF2B-TSS
-## 96 NCOA3-TSS
-## 97 PTPN1-TSS
-## 98 MIR155HG-TSS
-## 99 IGLL5-TSS
-## 100 TMSB4X-intronic
-## 101 PIM2-TSS
This plotting function is available for plotting one or multiple samples and takes either an already loaded MAF data frame or a MAF path. If none are supplied the function will get ssm data using one of the functions available in GAMBLR. There are also other convenient parameters for further customizing the returned plot. For example, we can label ASHM genes (label_ashm_genes = TRUE), subset to specific chromosomes, zoom in to regions of interest. If plot is restricted to specific chromosomes or zoomed in to a region, we can also add SV labels, with the labe_sv = TRUE. In this example, we are looking at one sample (HTMCP-01-06-0042-01A-01D), all chromosomes with ASHM genes labeled.
+diff --git a/docs/reference/cnvKompare-1.png b/docs/reference/cnvKompare-1.png index 449be8ac..ec9c408d 100644 Binary files a/docs/reference/cnvKompare-1.png and b/docs/reference/cnvKompare-1.png differ diff --git a/docs/reference/cnvKompare-2.png b/docs/reference/cnvKompare-2.png index 7b8283d8..8744cad6 100644 Binary files a/docs/reference/cnvKompare-2.png and b/docs/reference/cnvKompare-2.png differ diff --git a/docs/reference/cnvKompare.html b/docs/reference/cnvKompare.html index 1157b7aa..6d803c1c 100644 --- a/docs/reference/cnvKompare.html +++ b/docs/reference/cnvKompare.html @@ -113,7 +113,8 @@#build plot prettyRainfallPlot(this_sample_id = "HTMCP-01-06-00422-01A-01D", seq_type = "genome", @@ -748,7 +443,7 @@Rainfall PlotLollipop Plot
The function
-pretty_lollipop_plotis perfect for creating an appealing, flexible and interactive HTML-style lollipop plot from mutational data using a modified version of g3Lollipop function from g3viz package. This function only takes for parameters;maf_dfwhich is the data frame containing the mutations to be plotted.genethis parameter controls what gene to plot mutations for. Lastly,plot_titlelets you specify the name of the plot and withplot_themeyou can specify the plot theme. Please note that in order for this function to run, you must first installed the forked version of g3viz.+- - + +#get metadata (Fl and DLBCL) with pairing status matched metadata = get_gambl_metadata() %>% dplyr::filter(pairing_status == "matched") %>% @@ -764,14 +459,14 @@Lollipop Plot= "MYC", plot_title = "Mutation data for MYC", plot_theme = "nature2")
diff --git a/docs/reference/cleanup_maf.html b/docs/reference/cleanup_maf.html index 58d90fc1..3edbce91 100644 --- a/docs/reference/cleanup_maf.html +++ b/docs/reference/cleanup_maf.html @@ -127,9 +127,18 @@Mutation Frequency Bin Matrix
-
get_mutation_frequency_bin_matrixcounts the number of mutations in a sliding window across a region for all samples (in the provided metadata parameter) and clusters the data.diff --git a/docs/reference/calculate_pga.html b/docs/reference/calculate_pga.html index 33ddc2ae..c60e2604 100644 --- a/docs/reference/calculate_pga.html +++ b/docs/reference/calculate_pga.html @@ -154,44 +154,29 @@+#load metadata. dlbcl_bl_meta = get_gambl_metadata() %>% dplyr::filter(pathology %in% c("DLBCL", @@ -782,7 +477,7 @@Mutation Frequency Bin Matrix= dlbcl_bl_meta) %>% dplyr::filter(genetic_subgroup != "0")
-## /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsvdiff --git a/docs/reference/calc_mutation_frequency_sliding_windows.html b/docs/reference/calc_mutation_frequency_sliding_windows.html index b4ae2ead..f1735d12 100644 --- a/docs/reference/calc_mutation_frequency_sliding_windows.html +++ b/docs/reference/calc_mutation_frequency_sliding_windows.html @@ -211,9 +211,7 @@+diff --git a/docs/reference/assign_cn_to_ssm.html b/docs/reference/assign_cn_to_ssm.html index 09c9b967..bbbc1d9c 100644 --- a/docs/reference/assign_cn_to_ssm.html +++ b/docs/reference/assign_cn_to_ssm.html @@ -199,9 +199,8 @@#get ashm regions (grch37) and filter out a set of genes. some_regions = GAMBLR.data::somatic_hypermutation_locations_GRCh37_v_latest %>% dplyr::filter(!gene %in% c("BCL11A", "CD44", "CD74", "IRF1", "IRF4", @@ -833,7 +528,7 @@Mutation Frequency Bin MatrixOncoplots
Commonly, we will want to generate visualizations that only show genes deemed relevant for a given malignancy (and above some frequency threshold). For this purpose we have
-prettyOncoplotavailable. In the example bellow, we are looking at all coding SSM (genome samples) and the relevant genes for two malignancies (BL and DLBCL). This plotting function has a large collection of parameters that are available for further customization and manipulation of the returned plot. Please refer to the documentation for a complete explanation of each parameter.diff --git a/docs/reference/ashm_rainbow_plot.html b/docs/reference/ashm_rainbow_plot.html index a2e19d13..4118899c 100644 --- a/docs/reference/ashm_rainbow_plot.html +++ b/docs/reference/ashm_rainbow_plot.html @@ -171,14 +171,10 @@+-# Load the master merged MAF (coding only). It's usually more efficient to do this than to try to add filters to this query. Instead, just filter the data afterward maf_data = get_coding_ssm(seq_type = "genome") maf_metadata = get_gambl_metadata() @@ -845,8 +540,8 @@Oncoplots## --Possible FLAGS among top ten genes: ## TTN ## -Processing clinical data -## -Finished in 27.7s elapsed (55.4s cpu)
@@ -145,6 +146,10 @@+## -Finished in 28.4s elapsed (57.4s cpu)+#define some genes of interest bl_genes = c("NFKBIZ", "ID3", "TP53", "ARID1A", "FBXO11", "GNA13", "TCF3", "TFAP4", "HNRNPU", "FOXO1", @@ -893,7 +588,7 @@Oncoplots## [1] "numgenes: 18"
As previous stated,
-prettyOncoplothas many parameters that can be called to further customize the plot and aggregate the data that are to be plotted. In reality, if all features of this plotting functions were to be demonstrated, a dedicated vignette for this purpose might be the way to go. Even so, here is another example were we include non coding regions (3’ UTR, NFKBIZ).diff --git a/docs/reference/annotate_sv.html b/docs/reference/annotate_sv.html index d478ae6a..dce979b9 100644 --- a/docs/reference/annotate_sv.html +++ b/docs/reference/annotate_sv.html @@ -160,16 +160,14 @@+diff --git a/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-1.png b/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-1.png index 9a6108c6..6a22b485 100644 Binary files a/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-1.png and b/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-1.png differ diff --git a/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-2.png b/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-2.png index 02b19853..010ad3bb 100644 Binary files a/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-2.png and b/docs/articles/utilities_tutorial_files/figure-html/cnvKompare-2.png differ diff --git a/docs/articles/utilities_tutorial_files/figure-html/gene_cloud-1.png b/docs/articles/utilities_tutorial_files/figure-html/gene_cloud-1.png index 0203ab8a..5f9be7b6 100644 Binary files a/docs/articles/utilities_tutorial_files/figure-html/gene_cloud-1.png and b/docs/articles/utilities_tutorial_files/figure-html/gene_cloud-1.png differ diff --git a/docs/authors.html b/docs/authors.html index 0f34b96f..e0c19710 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -96,15 +96,15 @@-#get SSM for NFKBIZ UTR region nfkbiz_utr_region = "chr3:101,578,185-101,579,902" nfkbiz_ssm = get_ssm_by_region(region = nfkbiz_utr_region, seq_type = "genome", projection = "grch37", basic_columns = TRUE) @@ -908,8 +603,8 @@Oncoplots## --Possible FLAGS among top ten genes: ## TTN ## -Processing clinical data -## -Finished in 27.3s elapsed (54.9s cpu)
@@ -407,20 +408,20 @@+## -Finished in 28.3s elapsed (54.3s cpu)+@@ -203,7 +203,7 @@#create prettyOncoplot prettyOncoplot(maftools_obj = maf, genes = genes, diff --git a/docs/articles/ssm_tutorial_files/figure-html/ashm_multi-rainbow_plot-1.png b/docs/articles/ssm_tutorial_files/figure-html/ashm_multi-rainbow_plot-1.png index e7ba6692..db160812 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/ashm_multi-rainbow_plot-1.png and b/docs/articles/ssm_tutorial_files/figure-html/ashm_multi-rainbow_plot-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/ashm_rainbow_plot-1.png b/docs/articles/ssm_tutorial_files/figure-html/ashm_rainbow_plot-1.png index 4f9063fe..a93f8d1d 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/ashm_rainbow_plot-1.png and b/docs/articles/ssm_tutorial_files/figure-html/ashm_rainbow_plot-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/fancy_snv_chrdistplot-1.png b/docs/articles/ssm_tutorial_files/figure-html/fancy_snv_chrdistplot-1.png index 1dc50992..767f44e3 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/fancy_snv_chrdistplot-1.png and b/docs/articles/ssm_tutorial_files/figure-html/fancy_snv_chrdistplot-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/fancy_v_count-1.png b/docs/articles/ssm_tutorial_files/figure-html/fancy_v_count-1.png index 44df9b6a..8a4b39b2 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/fancy_v_count-1.png and b/docs/articles/ssm_tutorial_files/figure-html/fancy_v_count-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/get_mutation_frequency_bin_matrix-1.png b/docs/articles/ssm_tutorial_files/figure-html/get_mutation_frequency_bin_matrix-1.png index bf375493..b0fd2440 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/get_mutation_frequency_bin_matrix-1.png and b/docs/articles/ssm_tutorial_files/figure-html/get_mutation_frequency_bin_matrix-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/prettyRainfallPlot-1.png b/docs/articles/ssm_tutorial_files/figure-html/prettyRainfallPlot-1.png index 75fbbd05..2ddf0dde 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/prettyRainfallPlot-1.png and b/docs/articles/ssm_tutorial_files/figure-html/prettyRainfallPlot-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_1-1.png b/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_1-1.png index 698a88fc..6f5a7490 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_1-1.png and b/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_1-1.png differ diff --git a/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_2-1.png b/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_2-1.png index 0e0229e7..0bcf77cd 100644 Binary files a/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_2-1.png and b/docs/articles/ssm_tutorial_files/figure-html/pretty_oncoplot_2-1.png differ diff --git a/docs/articles/utilities_tutorial.html b/docs/articles/utilities_tutorial.html index 4b95fc11..d8a1fbc4 100644 --- a/docs/articles/utilities_tutorial.html +++ b/docs/articles/utilities_tutorial.html @@ -165,7 +165,7 @@Gene To Region
#gene to region, for multiple genes specified in an already subset list of gene names, return format is data frame #subset FL genes -fl_genes = dplyr::filter(lymphoma_genes_lymphoma_genes_v0.0, FL == TRUE) %>% pull(Gene) +fl_genes = dplyr::filter(lymphoma_genes_lymphoma_genes_v0.0, FL == TRUE) %>% pull(Gene) #get regions for Fl genes fl_genes_df = gene_to_region(gene_symbol = fl_genes, genome_build = "grch37", return_as = "df")Count SSM by Regionmy_region = gene_to_region(gene_symbol = "MYC", return_as = "region") #subset metadata. -my_metadata = get_gambl_metadata() %>% +my_metadata = get_gambl_metadata() %>% dplyr::filter(pathology == "FL") #count SSMs for the selected sample subset and defined region. @@ -227,7 +227,7 @@
Calculate Proportion of G
Interested to see the percentage of a genome altered by CNVs for specific sample, or sample subsets? For this purpose
calcualte_pgawas developed. This function takes into account the total length of sample’s CNV and relates it to the total genome length to return the proportion affected by CNV. The function can work with either individual or multi-sample seg files. The telomeres are always excluded from calculation, and centromeres/sex chromosomes can be optionally included or excluded.#get CN segments for a specific sample. -sample_seg = get_sample_cn_segments(this_sample_id = "14-36022T") %>% +sample_seg = get_sample_cn_segments(this_sample_id = "14-36022T") %>% dplyr::rename("sample" = "ID") #calculate PGA for the same sample. @@ -265,6 +265,7 @@Compare CNVs For Multiple Samples#get CNV comparison data. kompare_out = cnvKompare(patient_id = "13-26835", projection = "hg38", + show_x_labels = FALSE, genes_of_interest = c("EZH2", "TP53", "MYC", @@ -304,14 +305,14 @@
Collate Resultsgenome_collated = collate_results(seq_type_filter = "genome", from_cache = TRUE) #use an already subset metadata table for getting collated results (cached) -fl_metadata = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") +fl_metadata = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") fl_collated = collate_results(seq_type_filter = "genome", join_with_full_metadata = TRUE, these_samples_metadata = fl_metadata, from_cache = TRUE) #get collated results (cached) for all genome samples and join with full metadata everything_collated = collate_results(seq_type_filter = "genome", from_cache = TRUE, join_with_full_metadata = TRUE) #another example demonstrating correct usage of the sample_table parameter. -fl_samples = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") %>% dplyr::select(sample_id, patient_id, biopsy_id) +fl_samples = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") %>% dplyr::select(sample_id, patient_id, biopsy_id) fl_collated = collate_results(sample_table = fl_samples, seq_type_filter = "genome", from_cache = TRUE)
GAMBL Colours#print selected palettes to a ggplot object #get all gambl colours in a data frame format all_gambl_colours = get_gambl_colours(as_dataframe = TRUE) -classes = all_gambl_colours$group %>% +classes = all_gambl_colours$group %>% unique() #create a function for building the plots plot_this_colour = function(this_group){ - p = ggplot(dplyr::filter(all_gambl_colours, group == this_group), aes(x = name, y = 0, fill = colour, label = name)) + - geom_tile(width = 0.9, height = 1) + - geom_text(color = "white", fontface = "bold") + - scale_fill_identity(guide = "none") + - coord_flip() + - theme_void() + - labs(title = paste0(this_group)) + - theme(plot.title = element_text(lineheight = 0.9, hjust = 0.5, face = "bold")) + p = ggplot(dplyr::filter(all_gambl_colours, group == this_group), aes(x = name, y = 0, fill = colour, label = name)) + + geom_tile(width = 0.9, height = 1) + + geom_text(color = "white", fontface = "bold") + + scale_fill_identity(guide = "none") + + coord_flip() + + theme_void() + + labs(title = paste0(this_group)) + + theme(plot.title = element_text(lineheight = 0.9, hjust = 0.5, face = "bold")) p } @@ -505,9 +506,9 @@
Gene Cloudsmaf = get_coding_ssm(seq_type = "genome") #get gene symbols from MAF and subset to chr1 -maf_genes = dplyr::filter(maf, Hugo_Symbol != "Unknown") %>% - dplyr::filter(Chromosome == "1") %>% - pull(Hugo_Symbol) +maf_genes = dplyr::filter(maf, Hugo_Symbol != "Unknown") %>% + dplyr::filter(Chromosome == "1") %>% + pull(Hugo_Symbol) #build wordcloud prettyGeneCloud(maf_df = maf, these_genes = maf_genes)
Authors
- -
- -
Kostia Dreval. Author. +
- -
Laura Hilton. Contributor. +
- diff --git a/docs/function_index.html b/docs/function_index.html new file mode 100644 index 00000000..db4ccb83 --- /dev/null +++ b/docs/function_index.html @@ -0,0 +1,229 @@ + + + + + + + + + + + + + +
Function Index + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++ + + + ++ + + + + + + + + + + + + + + diff --git a/docs/index.html b/docs/index.html index 21d80ded..e0399fdb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -126,7 +126,7 @@ @@ -417,8 +417,8 @@+ + + ++ + +Function Index
+ +++ + + + +Where can I find the source code for any given GAMBLR function?
+Ever wondered where a specific function lives in the source code, or how any given function is being classified? For your convenience, here is a complete table with all currently available GAMBLR functions. Note that helper functions are not included in this list, since such functions are not exported to NAMESPACE. In addition, the bundled data sets are also not included.
+ + +Citation
Developers
-
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 051a6e37..450db738 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,9 +4,10 @@ pkgdown_sha: ~ articles: cn_sv_tutorial: cn_sv_tutorial.html fancy_plots: fancy_plots.html + function_index: function_index.html ssm_tutorial: ssm_tutorial.html utilities_tutorial: utilities_tutorial.html -last_built: 2023-06-08T17:16Z +last_built: 2023-06-12T19:19Z urls: reference: https://github.com/morinlab/GAMBLR/reference article: https://github.com/morinlab/GAMBLR/articles diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index f8f9e2ca..403b07b2 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 36562a00..65dd769b 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/add_icgc_metadata.html b/docs/reference/add_icgc_metadata.html deleted file mode 100644 index 330284b0..00000000 --- a/docs/reference/add_icgc_metadata.html +++ /dev/null @@ -1,117 +0,0 @@ - -- Ryan Morin
-
Author, maintainer- Kostia Dreval
+
Author- Ryan Morin
+
Author, maintainer- Kostia Dreval
Author- Adam Mattsson
Author- More about authors...
Add ICGC metadata. — add_icgc_metadata • GAMBLR - - --- - - - - - - - diff --git a/docs/reference/adjust_ploidy.html b/docs/reference/adjust_ploidy.html index 5ad76a77..9d56b445 100644 --- a/docs/reference/adjust_ploidy.html +++ b/docs/reference/adjust_ploidy.html @@ -158,40 +158,51 @@- - - - -- - --- --- -Add ICGC metadata.
- --add_icgc_metadata.Rd-- -Layer on ICGC metadata from a supplemental table to fill in missing COO.
--- --add_icgc_metadata(incoming_metadata)--Arguments
-
- incoming_metadata
-- - -
A metadata table (probably output from
get_gambl_metadata).--Value
- - -Metadata with layered information (ICGC).
--- -Details
-INTERNAL FUNCTION called by
-get_gambl_metadata, not meant for out-of-package usage.--Examples
--my_meta = get_gambl_metadata() -icgc_metadata = add_icgc_metadata(incoming_metadata = my_meta) -#> Error in add_icgc_metadata(incoming_metadata = my_meta): could not find function "add_icgc_metadata" - -Details
diff --git a/docs/reference/annotate_hotspots.html b/docs/reference/annotate_hotspots.html index 1c04b92c..4059400b 100644 --- a/docs/reference/annotate_hotspots.html +++ b/docs/reference/annotate_hotspots.html @@ -143,16 +143,16 @@Examples
sample_seg = get_sample_cn_segments(this_sample_id = "14-36022T") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. sample_seg = dplyr::rename(sample_seg, "sample" = "ID") -#> Error in dplyr::rename(sample_seg, sample = "ID"): object 'sample_seg' not found adjust_ploidy(this_seg = sample_seg) -#> Error in is.factor(x): object 'sample_seg' not found +#> Calculating PGA ... +#> Returning the seg file with ploidy-adjusted CN ... +#> # A tibble: 187 × 6 +#> sample chrom start end LOH_flag log.ratio +#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> +#> 1 14-36022T 1 10001 762600 0 0 +#> 2 14-36022T 1 762601 121500000 0 0 +#> 3 14-36022T 1 142600000 248277662 0 0 +#> 4 14-36022T 1 248277663 248278622 0 0 +#> 5 14-36022T 1 248278623 249226346 0 -1 +#> 6 14-36022T 1 249226347 249250620 0 0 +#> 7 14-36022T 2 10001 11319 0 0 +#> 8 14-36022T 2 11320 90500000 0 0 +#> 9 14-36022T 2 96800000 186704965 0 0 +#> 10 14-36022T 2 186704966 186712276 0 0 +#> # ℹ 177 more rows one_sample = get_sample_cn_segments(this_sample_id = "14-36022T") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. one_sample = dplyr::rename(one_sample, "sample" = "ID") -#> Error in dplyr::rename(one_sample, sample = "ID"): object 'one_sample' not found another_sample = get_sample_cn_segments(this_sample_id = "BLGSP-71-21-00243-01A-11E") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. another_sample = dplyr::rename(another_sample, "sample" = "ID") -#> Error in dplyr::rename(another_sample, sample = "ID"): object 'another_sample' not found multi_sample_seg = rbind(one_sample, another_sample) -#> Error in rbind(one_sample, another_sample): object 'one_sample' not found adjust_ploidy(this_seg = multi_sample_seg) -#> Error in is.factor(x): object 'multi_sample_seg' not found +#> Calculating PGA ... +#> Returning the seg file with ploidy-adjusted CN ... +#> # A tibble: 278 × 6 +#> sample chrom start end LOH_flag log.ratio +#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> +#> 1 14-36022T 1 10001 762600 0 0 +#> 2 14-36022T 1 762601 121500000 0 0 +#> 3 14-36022T 1 142600000 248277662 0 0 +#> 4 14-36022T 1 248277663 248278622 0 0 +#> 5 14-36022T 1 248278623 249226346 0 -1 +#> 6 14-36022T 1 249226347 249250620 0 0 +#> 7 14-36022T 2 10001 11319 0 0 +#> 8 14-36022T 2 11320 90500000 0 0 +#> 9 14-36022T 2 96800000 186704965 0 0 +#> 10 14-36022T 2 186704966 186712276 0 0 +#> # ℹ 268 more rowsDetails
diff --git a/docs/reference/annotate_igh_breakpoints.html b/docs/reference/annotate_igh_breakpoints.html index 32b687c0..61302557 100644 --- a/docs/reference/annotate_igh_breakpoints.html +++ b/docs/reference/annotate_igh_breakpoints.html @@ -128,14 +128,11 @@Examples
my_metadata = get_gambl_metadata() -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. all_coding_ssm = get_coding_ssm(these_samples_metadata = my_metadata, projection = "grch37", seq_type = "genome") -#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'my_metadata' not found +#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf +#> mutations from 1652 samples +#> after linking with metadata, we have mutations from 1646 samples hot_ssms = annotate_hotspots(all_coding_ssm) -#> Error: '/Users/rmorin/git/gambl/versioned_results/oncodriveclustl-0.0_FL--DLBCL_clusters_results.tsv' does not exist. +#> Adding missing grouping variables: `SYMBOL` +#> Adding missing grouping variables: `SYMBOL`Details
diff --git a/docs/reference/annotate_ssm_blacklist.html b/docs/reference/annotate_ssm_blacklist.html index fcb16699..f6a5c92b 100644 --- a/docs/reference/annotate_ssm_blacklist.html +++ b/docs/reference/annotate_ssm_blacklist.html @@ -200,10 +200,6 @@Examples
manta_sv = get_manta_sv(verbose = FALSE) -#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist. +#> WARNING! No SV calls found in flat-file for: 171116-PL02 +#> WARNING! No SV calls found in flat-file for: 171447-PL01 +#> WARNING! No SV calls found in flat-file for: 171451-PL01 all_annotated = annotate_sv(sv_data = manta_sv) -#> Error in dplyr::select(., "CHROM_A", "START_A", "END_A", "tumour_sample_id", ends_with("SCORE"), "STRAND_A"): object 'manta_sv' not found ig_annotated = annotate_igh_breakpoints(all_annotated) -#> Error in dplyr::filter(annotated_df, partner == "IGH"): object 'all_annotated' not foundExamples
deblacklisted_maf = annotate_ssm_blacklist(grande_maf, seq_type = "genome", genome_build = "hg38") -#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt' does not exist.Details
diff --git a/docs/reference/append_to_table.html b/docs/reference/append_to_table.html deleted file mode 100644 index 06c64efb..00000000 --- a/docs/reference/append_to_table.html +++ /dev/null @@ -1,121 +0,0 @@ - -Examples
sv_df = get_manta_sv(verbose = FALSE) -#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist. +#> WARNING! No SV calls found in flat-file for: 171116-PL02 +#> WARNING! No SV calls found in flat-file for: 171447-PL01 +#> WARNING! No SV calls found in flat-file for: 171451-PL01 annotated_entrez = annotate_sv(sv_data = sv_df, with_chr_prefix = FALSE, collapse_redundant = FALSE, return_as = "bedpe_entrez", genome_build = "grch37") -#> Error in dplyr::select(., "CHROM_A", "START_A", "END_A", "tumour_sample_id", ends_with("SCORE"), "STRAND_A"): object 'sv_df' not foundAppend To Table. — append_to_table • GAMBLR - - --- - - - - - - - diff --git a/docs/reference/ashm_multi_rainbow_plot-1.png b/docs/reference/ashm_multi_rainbow_plot-1.png index 235ce8ad..69c56e58 100644 Binary files a/docs/reference/ashm_multi_rainbow_plot-1.png and b/docs/reference/ashm_multi_rainbow_plot-1.png differ diff --git a/docs/reference/ashm_multi_rainbow_plot.html b/docs/reference/ashm_multi_rainbow_plot.html index c5aef055..ba7d2347 100644 --- a/docs/reference/ashm_multi_rainbow_plot.html +++ b/docs/reference/ashm_multi_rainbow_plot.html @@ -108,7 +108,8 @@- - - - -- - --- --- -Append To Table.
- --append_to_table.Rd-- -Housekeeping function to add results to a table.
--- --append_to_table(table_name, data_df)--Arguments
-
- table_name
-- - - -
The name of the database table to update/populate.
- data_df
-- - -
A dataframe of values to load into the table.
--Value
- - -A table.
--- -Details
-INTERNAL FUNCTION, not meant for out-of-package usage.
---Examples
--if (FALSE) { -table_up = append_to_table("my_table", "my_df") -} - -ASHM Multi-panel Rainbow Plot
seq_type, custom_colours, classification_column = "lymphgen", - maf_data + maf_data, + verbose = TRUE )Arguments
maf_data + + An already loaded maf, if no provided, this function will call
get_ssm_by_region, using the regions supplied intoregions_bed.verbose ++ Set to FALSE to rpevent printing the full regions bed file to the console. Default is TRUE.
Value
@@ -174,9 +179,316 @@Examples
"IGL"), custom_colours = lymphgen_colours, seq_type = "genome") -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. +#> chr_name hg19_start hg19_end gene region +#> 1 chr1 6661482 6662702 KLHL21 TSS +#> 2 chr1 23885584 23885835 ID3 TSS +#> 3 chr1 150550814 150552135 MCL1 intronic +#> 4 chr1 203274698 203275778 BTG2 intronic +#> 5 chr1 226864857 226873452 ITPKB intronic +#> 6 chr1 226920563 226927885 ITPKB TSS +#> 7 chr1 226921088 226927982 ITPKB intron-1 +#> 8 chr2 60773789 60783486 BCL11A TSS +#> 9 chr2 96808901 96811913 DUSP2 intron-1 +#> 10 chr2 111874854 111882174 BCL2L11 TSS +#> 11 chr2 136874728 136875461 CXCR4 intronic +#> 12 chr3 16546433 16556786 RFTN1 TSS +#> 13 chr3 32020518 32024930 OSBPL10 TSS-1 +#> 14 chr3 71104986 71119518 FOXP1 TSS-4 +#> 15 chr3 71176427 71180960 FOXP1 TSS-3 +#> 16 chr3 71350633 71357665 FOXP1 TSS-2 +#> 17 chr3 71503103 71504870 FOXP1 intron-1b +#> 18 chr3 71550753 71551478 FOXP1 intron-1a +#> 19 chr3 71626341 71635648 FOXP1 TSS-1 +#> 20 chr3 101546669 101547704 NFKBIZ TSS-1 +#> 21 chr3 101568239 101569274 NFKBIZ TSS-2 +#> 22 chr3 183269360 183274139 KLHL6 TSS +#> 23 chr3 186739628 186740875 ST6GAL1 TSS-1 +#> 24 chr3 186782522 186784438 ST6GAL1 intronic-1 +#> 25 chr3 187458526 187464632 BCL6 TSS +#> 26 chr3 187771678 187801626 LPP TSS-1 +#> 27 chr3 187801627 187813568 LPP TSS-2 +#> 28 chr3 187813569 187955254 LPP TSS-3 +#> 29 chr3 187955255 187969220 LPP TSS-4 +#> 30 chr3 188377178 188401951 LPP intronic-1 +#> 31 chr3 188401952 188461879 LPP intronic-2 +#> 32 chr3 188461880 188474683 LPP intronic-3 +#> 33 chr3 188474684 188491248 LPP intronic-4 +#> 34 chr4 40193105 40204231 RHOH TSS +#> 35 chr5 88131209 88174373 MEF2C TSS-3 +#> 36 chr5 88174374 88182243 MEF2C TSS-2 +#> 37 chr5 88182244 88206620 MEF2C TSS-1 +#> 38 chr5 131823933 131826458 IRF1 TSS +#> 39 chr5 149790977 149792349 CD74 TSS +#> 40 chr5 158500476 158532769 EBF1 TSS +#> 41 chr6 390572 394093 IRF4 TSS +#> 42 chr6 14118026 14120025 CD83 TSS +#> 43 chr6 31548325 31550717 LTB intron-1 +#> 44 chr6 37138104 37139804 PIM1 TSS +#> 45 chr6 90981034 91016134 BACH2 TSS +#> 46 chr6 134487960 134499859 SGK1 TSS-1 +#> 47 chr6 159237903 159240216 EZR TSS +#> 48 chr7 5568297 5570856 ACTB TSS +#> 49 chr8 11347723 11355318 BLK TSS +#> 50 chr8 128748352 128749427 MYC TSS +#> 51 chr9 37023396 37027663 PAX5 intron-1 +#> 52 chr9 37029849 37037154 PAX5 TSS-1 +#> 53 chr9 37192080 37207549 ZCCHC7 intron-4 +#> 54 chr9 37275952 37306152 ZCCHC7 intron-2 +#> 55 chr9 37312655 37328260 ZCCHC7 intron-3 +#> 56 chr9 37329706 37340398 ZCCHC7 intron-1 +#> 57 chr9 37369209 37372160 PAX5 distal-enhancer-1 +#> 58 chr9 37382267 37385854 PAX5 distal-enhancer-2 +#> 59 chr9 37395932 37409239 PAX5 distal-enhancer-3 +#> 60 chr9 37423010 37425279 GRHPR TSS +#> 61 chr10 127578912 127591133 FANK1 TSS +#> 62 chr11 9595246 9599502 WEE1 intronic +#> 63 chr11 35156769 35164248 CD44 TSS +#> 64 chr11 60223385 60225310 MS4A1 TSS +#> 65 chr11 65190369 65192380 NEAT1 ncRNA +#> 66 chr11 65265237 65268359 MALAT1 ncRNA +#> 67 chr11 102188170 102190077 BIRC3 TSS +#> 68 chr11 111248078 111250224 POU2AF1 TSS +#> 69 chr11 128339774 128345731 ETS1 introns +#> 70 chr11 128388492 128394163 ETS1 TSS-2 +#> 71 chr12 11796001 11812968 ETV6 TSS +#> 72 chr12 25204045 25213569 LRMP TSS +#> 73 chr12 92537999 92539598 BTG1 TSS +#> 74 chr12 113492311 113497546 DTX1 TSS +#> 75 chr12 122456912 122464036 BCL7A TSS +#> 76 chr13 46957278 46963342 C13orf18 TSS +#> 77 chr14 69257848 69259739 ZFP36L1 TSS +#> 78 chr14 94940587 94942549 SERPINA9 TSS +#> 79 chr14 96179535 96180366 TCL1A TSS +#> 80 chr15 59658991 59671152 MYO1E TSS +#> 81 chr16 10970795 10975465 CIITA TSS +#> 82 chr16 11347512 11350007 SOCS1 intron-1 +#> 83 chr16 27322895 27329423 IL4R TSS +#> 84 chr16 85931918 85933977 IRF8 TSS +#> 85 chr17 3597616 3599572 P2RX5 TSS +#> 86 chr17 56407732 56410140 TSPOAP1 intergenic +#> 87 chr17 75424734 75440956 SEPT9 intronic-1 +#> 88 chr17 75443766 75451177 SEPT9 intronic-2 +#> 89 chr17 75453203 75471471 SEPT9 intronic-3 +#> 90 chr17 79478289 79479959 ACTG1 intronic +#> 91 chr18 60796984 60814103 BCL2 intronic +#> 92 chr18 60982728 60988342 BCL2 TSS +#> 93 chr19 10340142 10341764 S1PR2 TSS +#> 94 chr19 16434978 16439011 KLF2 TSS +#> 95 chr19 19279635 19281441 MEF2B TSS +#> 96 chr20 46128611 46138099 NCOA3 TSS +#> 97 chr20 49120482 49140477 PTPN1 TSS +#> 98 chr21 26934372 26937651 MIR155HG TSS +#> 99 chr22 23229554 23232042 IGLL5 TSS +#> 100 chrX 12993308 12994511 TMSB4X intronic +#> 101 chrX 48774756 48776255 PIM2 TSS +#> regulatory_comment regions +#> 1 <NA> chr1:6661482-6662702 +#> 2 <NA> chr1:23885584-23885835 +#> 3 <NA> chr1:150550814-150552135 +#> 4 active_promoter chr1:203274698-203275778 +#> 5 weak_enhancer chr1:226864857-226873452 +#> 6 active_promoter chr1:226920563-226927885 +#> 7 enhancer chr1:226921088-226927982 +#> 8 active_promoter chr2:60773789-60783486 +#> 9 enhancer chr2:96808901-96811913 +#> 10 active_promoter chr2:111874854-111882174 +#> 11 weak_promoter chr2:136874728-136875461 +#> 12 active_promoter-strong_enhancer chr3:16546433-16556786 +#> 13 active_promoter chr3:32020518-32024930 +#> 14 active_promoter chr3:71104986-71119518 +#> 15 active_promoter chr3:71176427-71180960 +#> 16 active_promoter chr3:71350633-71357665 +#> 17 intronic chr3:71503103-71504870 +#> 18 intronic chr3:71550753-71551478 +#> 19 active_promoter chr3:71626341-71635648 +#> 20 active_promoter chr3:101546669-101547704 +#> 21 active_promoter chr3:101568239-101569274 +#> 22 active_promoter-strong_enhancer chr3:183269360-183274139 +#> 23 active_promoter chr3:186739628-186740875 +#> 24 strong_enhancer chr3:186782522-186784438 +#> 25 <NA> chr3:187458526-187464632 +#> 26 <NA> chr3:187771678-187801626 +#> 27 <NA> chr3:187801627-187813568 +#> 28 <NA> chr3:187813569-187955254 +#> 29 <NA> chr3:187955255-187969220 +#> 30 <NA> chr3:188377178-188401951 +#> 31 <NA> chr3:188401952-188461879 +#> 32 <NA> chr3:188461880-188474683 +#> 33 <NA> chr3:188474684-188491248 +#> 34 active_promoter chr4:40193105-40204231 +#> 35 active_promoter chr5:88131209-88174373 +#> 36 active_promoter chr5:88174374-88182243 +#> 37 active_promoter chr5:88182244-88206620 +#> 38 active_promoter chr5:131823933-131826458 +#> 39 active_promoter chr5:149790977-149792349 +#> 40 active_promoter chr5:158500476-158532769 +#> 41 active_promoter chr6:390572-394093 +#> 42 active_promoter-strong_enhancer chr6:14118026-14120025 +#> 43 enhancer chr6:31548325-31550717 +#> 44 active_promoter chr6:37138104-37139804 +#> 45 <NA> chr6:90981034-91016134 +#> 46 active_promoter chr6:134487960-134499859 +#> 47 <NA> chr6:159237903-159240216 +#> 48 active_promoter chr7:5568297-5570856 +#> 49 strong_enhancer chr8:11347723-11355318 +#> 50 active_promoter chr8:128748352-128749427 +#> 51 intronic chr9:37023396-37027663 +#> 52 active_promoter chr9:37029849-37037154 +#> 53 intronic chr9:37192080-37207549 +#> 54 intronic chr9:37275952-37306152 +#> 55 intronic chr9:37312655-37328260 +#> 56 intronic chr9:37329706-37340398 +#> 57 enhancer chr9:37369209-37372160 +#> 58 enhancer chr9:37382267-37385854 +#> 59 enhancer chr9:37395932-37409239 +#> 60 active_promoter chr9:37423010-37425279 +#> 61 active_promoter chr10:127578912-127591133 +#> 62 <NA> chr11:9595246-9599502 +#> 63 active_promoter chr11:35156769-35164248 +#> 64 active_promoter chr11:60223385-60225310 +#> 65 enhancer chr11:65190369-65192380 +#> 66 enhancer chr11:65265237-65268359 +#> 67 active_promoter chr11:102188170-102190077 +#> 68 active_promoter chr11:111248078-111250224 +#> 69 enhancer chr11:128339774-128345731 +#> 70 active_promoter chr11:128388492-128394163 +#> 71 strong_enhancer chr12:11796001-11812968 +#> 72 active_promoter chr12:25204045-25213569 +#> 73 active_promoter chr12:92537999-92539598 +#> 74 <NA> chr12:113492311-113497546 +#> 75 poised_promoter chr12:122456912-122464036 +#> 76 active_promoter chr13:46957278-46963342 +#> 77 active_promoter chr14:69257848-69259739 +#> 78 <NA> chr14:94940587-94942549 +#> 79 active_promoter chr14:96179535-96180366 +#> 80 <NA> chr15:59658991-59671152 +#> 81 active_promoter-strong_enhancer chr16:10970795-10975465 +#> 82 enhancer chr16:11347512-11350007 +#> 83 active_promoter chr16:27322895-27329423 +#> 84 active_promoter chr16:85931918-85933977 +#> 85 active_promoter chr17:3597616-3599572 +#> 86 enhancer chr17:56407732-56410140 +#> 87 active_promoter chr17:75424734-75440956 +#> 88 active_promoter chr17:75443766-75451177 +#> 89 active_promoter chr17:75453203-75471471 +#> 90 <NA> chr17:79478289-79479959 +#> 91 strong_enhancer chr18:60796984-60814103 +#> 92 active_promoter chr18:60982728-60988342 +#> 93 active_promoter chr19:10340142-10341764 +#> 94 intronic chr19:16434978-16439011 +#> 95 active_promoter chr19:19279635-19281441 +#> 96 active_promoter chr20:46128611-46138099 +#> 97 active_promoter chr20:49120482-49140477 +#> 98 active_promoter chr21:26934372-26937651 +#> 99 <NA> chr22:23229554-23232042 +#> 100 active_promoter chrX:12993308-12994511 +#> 101 active_promoter chrX:48774756-48776255 +#> name +#> 1 KLHL21-TSS +#> 2 ID3-TSS +#> 3 MCL1-intronic +#> 4 BTG2-intronic +#> 5 ITPKB-intronic +#> 6 ITPKB-TSS +#> 7 ITPKB-intron-1 +#> 8 BCL11A-TSS +#> 9 DUSP2-intron-1 +#> 10 BCL2L11-TSS +#> 11 CXCR4-intronic +#> 12 RFTN1-TSS +#> 13 OSBPL10-TSS-1 +#> 14 FOXP1-TSS-4 +#> 15 FOXP1-TSS-3 +#> 16 FOXP1-TSS-2 +#> 17 FOXP1-intron-1b +#> 18 FOXP1-intron-1a +#> 19 FOXP1-TSS-1 +#> 20 NFKBIZ-TSS-1 +#> 21 NFKBIZ-TSS-2 +#> 22 KLHL6-TSS +#> 23 ST6GAL1-TSS-1 +#> 24 ST6GAL1-intronic-1 +#> 25 BCL6-TSS +#> 26 LPP-TSS-1 +#> 27 LPP-TSS-2 +#> 28 LPP-TSS-3 +#> 29 LPP-TSS-4 +#> 30 LPP-intronic-1 +#> 31 LPP-intronic-2 +#> 32 LPP-intronic-3 +#> 33 LPP-intronic-4 +#> 34 RHOH-TSS +#> 35 MEF2C-TSS-3 +#> 36 MEF2C-TSS-2 +#> 37 MEF2C-TSS-1 +#> 38 IRF1-TSS +#> 39 CD74-TSS +#> 40 EBF1-TSS +#> 41 IRF4-TSS +#> 42 CD83-TSS +#> 43 LTB-intron-1 +#> 44 PIM1-TSS +#> 45 BACH2-TSS +#> 46 SGK1-TSS-1 +#> 47 EZR-TSS +#> 48 ACTB-TSS +#> 49 BLK-TSS +#> 50 MYC-TSS +#> 51 PAX5-intron-1 +#> 52 PAX5-TSS-1 +#> 53 ZCCHC7-intron-4 +#> 54 ZCCHC7-intron-2 +#> 55 ZCCHC7-intron-3 +#> 56 ZCCHC7-intron-1 +#> 57 PAX5-distal-enhancer-1 +#> 58 PAX5-distal-enhancer-2 +#> 59 PAX5-distal-enhancer-3 +#> 60 GRHPR-TSS +#> 61 FANK1-TSS +#> 62 WEE1-intronic +#> 63 CD44-TSS +#> 64 MS4A1-TSS +#> 65 NEAT1-ncRNA +#> 66 MALAT1-ncRNA +#> 67 BIRC3-TSS +#> 68 POU2AF1-TSS +#> 69 ETS1-introns +#> 70 ETS1-TSS-2 +#> 71 ETV6-TSS +#> 72 LRMP-TSS +#> 73 BTG1-TSS +#> 74 DTX1-TSS +#> 75 BCL7A-TSS +#> 76 C13orf18-TSS +#> 77 ZFP36L1-TSS +#> 78 SERPINA9-TSS +#> 79 TCL1A-TSS +#> 80 MYO1E-TSS +#> 81 CIITA-TSS +#> 82 SOCS1-intron-1 +#> 83 IL4R-TSS +#> 84 IRF8-TSS +#> 85 P2RX5-TSS +#> 86 TSPOAP1-intergenic +#> 87 SEPT9-intronic-1 +#> 88 SEPT9-intronic-2 +#> 89 SEPT9-intronic-3 +#> 90 ACTG1-intronic +#> 91 BCL2-intronic +#> 92 BCL2-TSS +#> 93 S1PR2-TSS +#> 94 KLF2-TSS +#> 95 MEF2B-TSS +#> 96 NCOA3-TSS +#> 97 PTPN1-TSS +#> 98 MIR155HG-TSS +#> 99 IGLL5-TSS +#> 100 TMSB4X-intronic +#> 101 PIM2-TSS +#> Joining with `by = join_by(sample_id)` +#> Joining with `by = join_by(start)` +#> Joining with `by = join_by(sample_id)` +
Examples
#basic usage this_region = "chr6:90975034-91066134" this_metadata = get_gambl_metadata() -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. ashm_rainbow_plot(metadata = this_metadata, region = this_region) -#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.maf.bgz" -#> Error in get_ssm_by_region(region = region, streamlined = TRUE, from_indexed_flatfile = T): failed to find the file needed for this +
Details
Examples
cn_list = assign_cn_to_ssm(this_sample_id = "HTMCP-01-06-00422-01A-01D", coding_only = TRUE) -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. +#> trying to find output from: battenberg +#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.segExamples
chr11_mut_freq = calc_mutation_frequency_sliding_windows(this_region = "chr11:69455000-69459900", slide_by = 10, window_size = 10000) -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. +#> processing bins of size 10000 across 4900 bp regionDetails
diff --git a/docs/reference/check_config_value.html b/docs/reference/check_config_value.html deleted file mode 100644 index 6a8909fe..00000000 --- a/docs/reference/check_config_value.html +++ /dev/null @@ -1,118 +0,0 @@ - -Examples
sample_seg = get_sample_cn_segments(this_sample_id = "14-36022T") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. sample_seg = dplyr::rename(sample_seg, "sample" = "ID") -#> Error in dplyr::rename(sample_seg, sample = "ID"): object 'sample_seg' not found calculate_pga(this_seg = sample_seg) -#> Error in distinct(., sample): object 'sample_seg' not found +#> sample_id PGA +#> 1 14-36022T 0.871 calculate_pga(this_seg = sample_seg, exclude_sex = FALSE) -#> Error in distinct(., sample): object 'sample_seg' not found +#> sample_id PGA +#> 1 14-36022T 0.866 one_sample = get_sample_cn_segments(this_sample_id = "14-36022T") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. one_sample = dplyr::rename(one_sample, "sample" = "ID") -#> Error in dplyr::rename(one_sample, sample = "ID"): object 'one_sample' not found another_sample = get_sample_cn_segments(this_sample_id = "BLGSP-71-21-00243-01A-11E") -#> restricting to non-ICGC data -#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg" -#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files? -#> Sys.setenv(R_CONFIG_ACTIVE = "remote") -#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist. another_sample = dplyr::rename(another_sample, "sample" = "ID") -#> Error in dplyr::rename(another_sample, sample = "ID"): object 'another_sample' not found multi_sample_seg = rbind(one_sample, another_sample) -#> Error in rbind(one_sample, another_sample): object 'one_sample' not found calculate_pga(this_seg = multi_sample_seg) -#> Error in distinct(., sample): object 'multi_sample_seg' not found +#> sample_id PGA +#> 1 14-36022T 0.871 +#> 2 BLGSP-71-21-00243-01A-11E 0.000Check Config Value. — check_config_value • GAMBLR - - --- - - - - - - - diff --git a/docs/reference/check_gambl_metadata.html b/docs/reference/check_gambl_metadata.html index 89eec3ed..ff98b097 100644 --- a/docs/reference/check_gambl_metadata.html +++ b/docs/reference/check_gambl_metadata.html @@ -135,11 +135,24 @@- - - - -- - --- --- -Check Config Value.
- --check_config_value.Rd-- -Check the existence of a specific config key. -The function will notify the user and end the program if no such key exists.
--- --check_config_value(config_key)--Arguments
-
- config_key
-- - -
key from config, prefixed with config::get()
--Value
- - -A string with the path to a file specified in the config or nothing (if config key is NULL).
--- -Details
-INTERNAL FUNCTION for checking the existence of a config value, not meant for out-of-package usage.
---Examples
--check_config_value(config::get("resources")$blacklist$template) -#> Error in check_config_value(config::get("resources")$blacklist$template): could not find function "check_config_value" - -Details
diff --git a/docs/reference/check_gamblr_config.html b/docs/reference/check_gamblr_config.html index 991dc73b..6f3f21d6 100644 --- a/docs/reference/check_gamblr_config.html +++ b/docs/reference/check_gamblr_config.html @@ -153,74 +153,50 @@Examples
this_metadata = get_gambl_metadata() -#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv" -#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config? -#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist. check_gambl_metadata(metadata_df = this_metadata) -#> Error in h(simpleError(msg, call)): error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'colnames': object 'this_metadata' not found +#> PASSED uniqueness test for sample_id +#> COO_consensus OK +#> DHITsig_consensus OK +#> possible problem! +#> [1] "0.299 % of values not assigned to an available colour." +#> possible problem! +#> [1] "7.899 % of values not assigned to an available colour." +#> possible problem! +#> [1] "11.67 % of values not assigned to an available colour." +#> possible problem! +#> [1] "71.813 % of values not assigned to an available colour." +#> possible problem! +#> [1] "66.308 % of values not assigned to an available colour." +#> possible problem! +#> [1] "70.796 % of values not assigned to an available colour." +#> possible problem! +#> [1] "100 % of values not assigned to an available colour."Examples
#> [1] "all_the_things/cnv_master-1.0/merges/{seq_type}--{projection}.seg" #> Warning: argument is not an atomic vector; coercing #> [1] "all_the_things/svar_master-1.0/merges/gridss_manta.genome--{projection}.bedpe" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--grch37_clean_blacklist.txt -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--grch37_clean_blacklist.txt" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--hg38_clean_blacklist.txt -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--hg38_clean_blacklist.txt" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--grch37_clean_blacklist.txt -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--grch37_clean_blacklist.txt" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt" -#> Looking for: /Users/rmorin/gambl_results/shared/gambl_capture_results.tsv -#> [1] "/Users/rmorin/gambl_results/shared/gambl_capture_results.tsv" -#> Looking for: /Users/rmorin/gambl_results/shared/gambl_genome_results.tsv -#> [1] "/Users/rmorin/gambl_results/shared/gambl_genome_results.tsv" -#> Looking for: /Users/rmorin/gambl_results/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv.gz -#> [1] "/Users/rmorin/gambl_results/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv.gz" -#> Looking for: /Users/rmorin/gambl_results/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv -#> [1] "/Users/rmorin/gambl_results/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--grch37.seg -#> [1] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--grch37.seg" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--hg38.seg -#> [1] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--hg38.seg" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--grch37.seg -#> [1] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--grch37.seg" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--hg38.seg -#> [1] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--hg38.seg" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe -#> [1] "/Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe" -#> Looking for: /Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--hg38.bedpe -#> [1] "/Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--hg38.bedpe" -#> Warning: There were 22 files that cannot be found (see above). If this is unexpected, try to obtain them. -#> [1] "MISSING FILES:" -#> [1] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--grch37_clean_blacklist.txt" -#> [2] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--hg38_clean_blacklist.txt" -#> [3] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--grch37_clean_blacklist.txt" -#> [4] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt" -#> [5] "/Users/rmorin/gambl_results/shared/gambl_capture_results.tsv" -#> [6] "/Users/rmorin/gambl_results/shared/gambl_genome_results.tsv" -#> [7] "/Users/rmorin/gambl_results/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv.gz" -#> [8] "/Users/rmorin/gambl_results/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv" -#> [9] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf" -#> [10] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf" -#> [11] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf" -#> [12] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf" -#> [13] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf" -#> [14] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf" -#> [15] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf" -#> [16] "/Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf" -#> [17] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--grch37.seg" -#> [18] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/capture--hg38.seg" -#> [19] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--grch37.seg" -#> [20] "/Users/rmorin/gambl_results/all_the_things/cnv_master-1.0/merges/genome--hg38.seg" -#> [21] "/Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe" -#> [22] "/Users/rmorin/gambl_results/all_the_things/svar_master-1.0/merges/gridss_manta.genome--hg38.bedpe" +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--grch37_clean_blacklist.txt +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/capture--hg38_clean_blacklist.txt +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--grch37_clean_blacklist.txt +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/level_3/genome--hg38_clean_blacklist.txt +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_capture_results.tsv +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv.gz +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--grch37.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/maf/all_slms-3--hg38.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--hg38.CDS.maf +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/capture--grch37.seg +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/capture--hg38.seg +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/genome--grch37.seg +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/cnv_master-1.0/merges/genome--hg38.seg +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe +#> OK +#> Looking for: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/svar_master-1.0/merges/gridss_manta.genome--hg38.bedpe +#> OK #> [1] "DONE!"Details
Examples
clean_maf = cleanup_maf(maf_df = grande_maf) -#> Warning: NAs introduced by coercion -#> Warning: NAs introduced by coercion -#> Warning: NAs introduced by coercion +#> Warning: There was 1 warning in `mutate()`. +#> ℹ In argument: `CDS_position = as.numeric(as.character(CDS_position))`. +#> Caused by warning: +#> ! NAs introduced by coercion +#> Warning: There was 1 warning in `mutate()`. +#> ℹ In argument: `cDNA_position = as.numeric(as.character(cDNA_position))`. +#> Caused by warning: +#> ! NAs introduced by coercion +#> Warning: There was 1 warning in `mutate()`. +#> ℹ In argument: `Protein_position = as.numeric(as.character(Protein_position))`. +#> Caused by warning: +#> ! NAs introduced by coercionCompare segmented data for multiple samples.
min_concordance = 90, exclude_sex = FALSE, return_heatmap = TRUE, - compare_pairwise = TRUE + compare_pairwise = TRUE, + show_x_labels = TRUE )
Boolean argument specifying whether to perform pairwise comparisons if there are more than 2 time points in the group. Default is TRUE.
Optional boolean parameter for hiding/showing x axis labels, default is TRUE.
+#>
+#> $time_plot
+
+#>
+#> $pairwise_comparisons
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorB`
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorB`$pairwise_concordance_pct
+#> [1] 4.17
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorB`$concordant_cytobands
+#> # A tibble: 66 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorA chr13 31600000 33400000 chr13_q13.1 200
+#> 2 13-26835_tumorB chr13 31600000 33400000 chr13_q13.1 200
+#> 3 13-26835_tumorA chr13 33400000 34900000 chr13_q13.2 200
+#> 4 13-26835_tumorB chr13 33400000 34900000 chr13_q13.2 200
+#> 5 13-26835_tumorA chr13 34900000 39500000 chr13_q13.3 200
+#> 6 13-26835_tumorB chr13 34900000 39500000 chr13_q13.3 200
+#> 7 13-26835_tumorA chr13 39500000 44600000 chr13_q14.11 200
+#> 8 13-26835_tumorB chr13 39500000 44600000 chr13_q14.11 200
+#> 9 13-26835_tumorA chr13 44600000 45200000 chr13_q14.12 200
+#> 10 13-26835_tumorB chr13 44600000 45200000 chr13_q14.12 200
+#> # ℹ 56 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorB`$discordant_cytobands
+#> # A tibble: 1,518 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 0 200
+#> 2 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 0.585 300
+#> 3 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 0 200
+#> 4 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 0.585 300
+#> 5 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 0 200
+#> 6 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 0.585 300
+#> 7 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 0 200
+#> 8 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 0.585 300
+#> 9 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 0 200
+#> 10 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 0.585 300
+#> # ℹ 1,508 more rows
+#>
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorC`
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorC`$pairwise_concordance_pct
+#> [1] 88.13
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorC`$concordant_cytobands
+#> # A tibble: 1,396 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorA chr10 34200000 38000000 chr10_p11.21 200
+#> 2 13-26835_tumorC chr10 34200000 38000000 chr10_p11.21 200
+#> 3 13-26835_tumorA chr10 31100000 34200000 chr10_p11.22 200
+#> 4 13-26835_tumorC chr10 31100000 34200000 chr10_p11.22 200
+#> 5 13-26835_tumorA chr10 29300000 31100000 chr10_p11.23 200
+#> 6 13-26835_tumorC chr10 29300000 31100000 chr10_p11.23 200
+#> 7 13-26835_tumorA chr10 24300000 29300000 chr10_p12.1 200
+#> 8 13-26835_tumorC chr10 24300000 29300000 chr10_p12.1 200
+#> 9 13-26835_tumorA chr10 22300000 24300000 chr10_p12.2 200
+#> 10 13-26835_tumorC chr10 22300000 24300000 chr10_p12.2 200
+#> # ℹ 1,386 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorC`$discordant_cytobands
+#> # A tibble: 188 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr11 48800000 5.10e7 chr1… 100 0.585 250
+#> 2 13-26835_tum… chr11 48800000 5.10e7 chr1… 100 -0.219 200
+#> 3 13-26835_tum… chr11 43400000 4.88e7 chr1… 100 0.585 300
+#> 4 13-26835_tum… chr11 43400000 4.88e7 chr1… 100 -0.219 200
+#> 5 13-26835_tum… chr11 36400000 4.34e7 chr1… 100 0.585 300
+#> 6 13-26835_tum… chr11 36400000 4.34e7 chr1… 100 -0.219 200
+#> 7 13-26835_tum… chr11 31000000 3.64e7 chr1… 100 0.585 300
+#> 8 13-26835_tum… chr11 31000000 3.64e7 chr1… 100 -0.219 200
+#> 9 13-26835_tum… chr11 27200000 3.10e7 chr1… 100 0.585 300
+#> 10 13-26835_tum… chr11 27200000 3.10e7 chr1… 100 -0.219 200
+#> # ℹ 178 more rows
+#>
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorD`
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorD`$pairwise_concordance_pct
+#> [1] 81.44
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorD`$concordant_cytobands
+#> # A tibble: 1,290 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorA chr10 34200000 38000000 chr10_p11.21 200
+#> 2 13-26835_tumorD chr10 34200000 38000000 chr10_p11.21 200
+#> 3 13-26835_tumorA chr10 31100000 34200000 chr10_p11.22 200
+#> 4 13-26835_tumorD chr10 31100000 34200000 chr10_p11.22 200
+#> 5 13-26835_tumorA chr10 29300000 31100000 chr10_p11.23 200
+#> 6 13-26835_tumorD chr10 29300000 31100000 chr10_p11.23 200
+#> 7 13-26835_tumorA chr10 24300000 29300000 chr10_p12.1 200
+#> 8 13-26835_tumorD chr10 24300000 29300000 chr10_p12.1 200
+#> 9 13-26835_tumorA chr10 22300000 24300000 chr10_p12.2 200
+#> 10 13-26835_tumorD chr10 22300000 24300000 chr10_p12.2 200
+#> # ℹ 1,280 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorA--13-26835_tumorD`$discordant_cytobands
+#> # A tibble: 294 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr11 48800000 5.10e7 chr1… 100 0.585 250
+#> 2 13-26835_tum… chr11 48800000 5.10e7 chr1… 100 0 200
+#> 3 13-26835_tum… chr11 43400000 4.88e7 chr1… 100 0.585 300
+#> 4 13-26835_tum… chr11 43400000 4.88e7 chr1… 100 0 200
+#> 5 13-26835_tum… chr11 36400000 4.34e7 chr1… 100 0.585 300
+#> 6 13-26835_tum… chr11 36400000 4.34e7 chr1… 100 0 200
+#> 7 13-26835_tum… chr11 31000000 3.64e7 chr1… 100 0.585 300
+#> 8 13-26835_tum… chr11 31000000 3.64e7 chr1… 100 0 200
+#> 9 13-26835_tum… chr11 27200000 3.10e7 chr1… 100 0.585 300
+#> 10 13-26835_tum… chr11 27200000 3.10e7 chr1… 100 0 200
+#> # ℹ 284 more rows
+#>
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorC`
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorC`$pairwise_concordance_pct
+#> [1] 3.16
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorC`$concordant_cytobands
+#> # A tibble: 50 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorB chr15 20500000 25500000 chr15_q11.2 200
+#> 2 13-26835_tumorC chr15 20500000 25500000 chr15_q11.2 200
+#> 3 13-26835_tumorB chr15 25500000 27800000 chr15_q12 200
+#> 4 13-26835_tumorC chr15 25500000 27800000 chr15_q12 200
+#> 5 13-26835_tumorB chr15 27800000 30000000 chr15_q13.1 200
+#> 6 13-26835_tumorC chr15 27800000 30000000 chr15_q13.1 200
+#> 7 13-26835_tumorB chr15 30000000 30900000 chr15_q13.2 200
+#> 8 13-26835_tumorC chr15 30000000 30900000 chr15_q13.2 200
+#> 9 13-26835_tumorB chr15 30900000 33400000 chr15_q13.3 200
+#> 10 13-26835_tumorC chr15 30900000 33400000 chr15_q13.3 200
+#> # ℹ 40 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorC`$discordant_cytobands
+#> # A tibble: 1,534 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 0.585 300
+#> 2 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 -0.180 200
+#> 3 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 0.585 300
+#> 4 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 -0.180 200
+#> 5 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 0.585 300
+#> 6 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 -0.180 200
+#> 7 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 0.585 300
+#> 8 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 -0.180 200
+#> 9 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 0.585 300
+#> 10 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 -0.180 200
+#> # ℹ 1,524 more rows
+#>
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorD`
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorD`$pairwise_concordance_pct
+#> [1] 7.07
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorD`$concordant_cytobands
+#> # A tibble: 112 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorB chr12 30500000 33200000 chr12_p11.21 400
+#> 2 13-26835_tumorD chr12 30500000 33200000 chr12_p11.21 400
+#> 3 13-26835_tumorB chr12 27600000 30500000 chr12_p11.22 400
+#> 4 13-26835_tumorD chr12 27600000 30500000 chr12_p11.22 400
+#> 5 13-26835_tumorB chr12 26300000 27600000 chr12_p11.23 400
+#> 6 13-26835_tumorD chr12 26300000 27600000 chr12_p11.23 400
+#> 7 13-26835_tumorB chr12 21100000 26300000 chr12_p12.1 400
+#> 8 13-26835_tumorD chr12 21100000 26300000 chr12_p12.1 400
+#> 9 13-26835_tumorB chr12 19800000 21100000 chr12_p12.2 400
+#> 10 13-26835_tumorD chr12 19800000 21100000 chr12_p12.2 400
+#> # ℹ 102 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorB--13-26835_tumorD`$discordant_cytobands
+#> # A tibble: 1,472 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 0.585 300
+#> 2 13-26835_tum… chr10 34200000 3.8 e7 chr1… 100 0 200
+#> 3 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 0.585 300
+#> 4 13-26835_tum… chr10 31100000 3.42e7 chr1… 100 0 200
+#> 5 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 0.585 300
+#> 6 13-26835_tum… chr10 29300000 3.11e7 chr1… 100 0 200
+#> 7 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 0.585 300
+#> 8 13-26835_tum… chr10 24300000 2.93e7 chr1… 100 0 200
+#> 9 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 0.585 300
+#> 10 13-26835_tum… chr10 22300000 2.43e7 chr1… 100 0 200
+#> # ℹ 1,462 more rows
+#>
+#>
+#> $pairwise_comparisons$`13-26835_tumorC--13-26835_tumorD`
+#> $pairwise_comparisons$`13-26835_tumorC--13-26835_tumorD`$pairwise_concordance_pct
+#> [1] 85.1
+#>
+#> $pairwise_comparisons$`13-26835_tumorC--13-26835_tumorD`$concordant_cytobands
+#> # A tibble: 1,348 × 6
+#> ID cb.chromosome cb.start cb.end name score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl>
+#> 1 13-26835_tumorC chr10 34200000 38000000 chr10_p11.21 200
+#> 2 13-26835_tumorD chr10 34200000 38000000 chr10_p11.21 200
+#> 3 13-26835_tumorC chr10 31100000 34200000 chr10_p11.22 200
+#> 4 13-26835_tumorD chr10 31100000 34200000 chr10_p11.22 200
+#> 5 13-26835_tumorC chr10 29300000 31100000 chr10_p11.23 200
+#> 6 13-26835_tumorD chr10 29300000 31100000 chr10_p11.23 200
+#> 7 13-26835_tumorC chr10 24300000 29300000 chr10_p12.1 200
+#> 8 13-26835_tumorD chr10 24300000 29300000 chr10_p12.1 200
+#> 9 13-26835_tumorC chr10 22300000 24300000 chr10_p12.2 200
+#> 10 13-26835_tumorD chr10 22300000 24300000 chr10_p12.2 200
+#> # ℹ 1,338 more rows
+#>
+#> $pairwise_comparisons$`13-26835_tumorC--13-26835_tumorD`$discordant_cytobands
+#> # A tibble: 236 × 8
+#> ID cb.chromosome cb.start cb.end name pct_covered log.ratio score
+#> <chr> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 13-26835_tum… chr11 2.8 e6 1.17e7 chr1… 100 0.585 233.
+#> 2 13-26835_tum… chr11 2.8 e6 1.17e7 chr1… 100 0 200
+#> 3 13-26835_tum… chr11 0 2.8 e6 chr1… 100 0 250
+#> 4 13-26835_tum… chr11 0 2.8 e6 chr1… 100 0 200
+#> 5 13-26835_tum… chr11 1.03e8 1.11e8 chr1… 100 -0.180 200
+#> 6 13-26835_tum… chr11 1.03e8 1.11e8 chr1… 100 0 233.
+#> 7 13-26835_tum… chr11 1.11e8 1.13e8 chr1… 100 -0.180 200
+#> 8 13-26835_tum… chr11 1.11e8 1.13e8 chr1… 100 0.585 300
+#> 9 13-26835_tum… chr11 1.13e8 1.15e8 chr1… 100 -0.180 200
+#> 10 13-26835_tum… chr11 1.13e8 1.15e8 chr1… 100 0.585 300
+#> # ℹ 226 more rows
+#>
+#>
+#>
collate_ancestry.RdGather ancestry information and expand the incoming sample table (or metadata).
-collate_ancestry(sample_table, seq_type_filter = "genome", somalier_output)A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Somalier ancestery.tsv
A table.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-table = collate_ancestry(sample_table = "my_sample_table.txt")
-}
-
-collate_ashm_results.RdDetermine the hypermutation status of a few genes.
-collate_ashm_results(sample_table, seq_type_filter = "genome")A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Samples table.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-sample_table = collate_ashm_results(sample_table = sample_table)
-}
-
-collate_csr_results.RdCollate a few CSR annotations, including MiXCR.
-collate_csr_results(sample_table, seq_type_filter = "genome")A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
The sample table with additional columns.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
-if (FALSE) {
-gambl_results_derived = collate_csr_results(gambl_results_derived)
-}
-
-collate_curated_sv_results.RdCollate all SV calls from the genome data and summarize for main oncogenes of interest per sample.
-collate_curated_sv_results(sample_table, seq_type_filter = "genome")A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
The sample table with additional columns.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
-if (FALSE) {
-gambl_results_derived = collate_curated_sv_results(gambl_results_derived)
-}
-
-collate_derived_results.RdExtract derived results stored in the database (these are usually slower to derive on the fly).
-collate_derived_results(
- sample_table,
- seq_type_filter = "genome",
- from_flatfile = FALSE
-)A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Optional argument whether to use database or flat file to retrieve mutations. Default is FALSE, TRUE is not yet implemented.
Data frame with one row per sample. Contains the contents of the derived_data table in the database.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
-if (FALSE) {
-gambl_results_derived = collate_derived_results(samples_df)
-}
-collate_extra_metadata.RdGather additional metadata information and expand the incoming sample table (or metadata).
-collate_extra_metadata(sample_table, file_path)A data frame with sample_id as the first column.
Path to extra metadata.
A table.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-table = collate_extra_metadata(sample_table = "my_sample_table.txt")
-}
-
-this_meta = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
dlbcl_meta = dplyr::filter(this_meta, pathology == "DLBCL")
-#> Error in dplyr::filter(this_meta, pathology == "DLBCL"): object 'this_meta' not found
wide_lymphgen = collate_lymphgen(these_samples_metadata = dlbcl_meta,
lymphgen_version = "default",
tidy = FALSE)
-#> Error in mutate(df, `:=`({ { lymphgen_column_out }}, case_when(!str_detect(.data[[lymphgen_column_in]], "/") ~ .data[[lymphgen_column_in]], str_detect(.data[[lymphgen_column_in]], "EZB") ~ "EZB-COMP", str_detect(.data[[lymphgen_column_in]], "MCD") ~ "MCD-COMP", str_detect(.data[[lymphgen_column_in]], "N1") ~ "N1-COMP", str_detect(.data[[lymphgen_column_in]], "BN2") ~ "BN2-COMP", str_detect(.data[[lymphgen_column_in]], "ST2") ~ "ST2-COMP"))): Problem while computing `LymphGen = case_when(...)`.
-#> Caused by error in `.data[["Subtype.Prediction"]]`:
-#> ! Column `Subtype.Prediction` not found in `.data`.
+#> Joining with `by = join_by(sample_id)`
collate_nfkbiz_results.RdDetermine which cases have NFKBIZ UTR mutations.
-collate_nfkbiz_results(sample_table, seq_type_filter = "genome")A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Samples table.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-sample_table = collate_nfkbiz_results(sample_table = sample_table)
-}
-
-collate_qc_results.RdExpand a metadata table horizontally with quality control metrics.
-collate_qc_results(sample_table, seq_type_filter = "genome")df with sample ids in the first column.
default is genome, capture is also available for unix_group icgc_dart.
The sample table with additional columns.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-qc_metrics = collate_qc_results(sample_table = sample_table)
-}
-
-collate_sbs_results.RdBring in the results from mutational signature analysis.
-collate_sbs_results(
- sample_table,
- seq_type_filter = "genome",
- file_path,
- scale_vals = FALSE,
- sbs_manipulation = ""
-)A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Optional path to SBS file.
Parameter not used?
Optional variable for transforming sbs values (e.g log, scale).
A data frame with new columns added.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-collated = collate_sbs_results(sample_table = sample_table,
- sbs_manipulation = sbs_manipulation)
-}
-collate_ssm_results.RdCompute summary statistics based on SSM calls.
-collate_ssm_results(
- sample_table,
- seq_type_filter = "genome",
- projection = "grch37",
- from_flatfile = TRUE,
- include_silent = FALSE
-)A data frame with sample_id as the first column.
Filtering criteria, default is genomes.
Specifies the projection, default is "grch37".
Optional argument whether to use database or flat file to retrieve mutations, default is TRUE.
Logical parameter indicating whether to include silent mutations into coding mutations. Default is FALSE.
The sample table with additional columns.
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
-if (FALSE) {
-ssm_results = colalte_ssm_results(sample_table = samples,
- include_silent = TRUE)
-}
-
-collate_sv_results.RdDetermine and summarize which cases have specific oncogene SVs.
-collate_sv_results(
- sample_table,
- tool = "manta",
- seq_type_filter = "genome",
- oncogenes = c("MYC", "BCL2", "BCL6", "CCND1", "IRF4")
-)A data frame with sample_id as the first column.
Name of tool (optional, default is manta).
Filtering criteria, default is genomes.
Which oncogenes to collate SVs from.
Data frame with additional columns (tooloncogene and tooloncogene_partner).
-INTERNAL FUNCTION called by collate_results, not meant for out-of-package usage.
if (FALSE) {
-results = collate_samples_sv_results(sample_table = samples,
- tool = "manta",
- oncogenes = c("MYC", "BCL2"))
-}
-
-compare_mutation_flavour.RdGet a MAF that is just the variants unique to one of two flavours of variant calls available.
-compare_mutation_flavour(
- these_sample_ids,
- flavour1 = "clustered",
- flavour2 = ""
-)A vector of sample IDs to be included.
First flavour of variant calls, to be returned as unique if not present in flavour2. Default is "clustered".
Second flavour of variant calls.
a list with MAFs that are only present in flavour1.
-Subset a MAF to only have variants that are unique to one flavour (specified with flavour1).
-This function is currently not exported, since there is only one flavour available at the moment (see docs for get_ssm_by_sample).
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
consolidate_lymphgen(sample_table = metadata)
-#> No external data path was provided, using default path /Users/rmorin/gambl_results/icgc_dart/derived_and_curated_metadata/
-#> No file(s) with lymphgen information were found at the path
-#> If you expected the data to be present at the specified location, please ensure they follow naming convention *.lymphgen.txt
-#> Error in consolidate_lymphgen(sample_table = metadata): object 'metadata' not found
+#> No external data path was provided, using default path /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/derived_and_curated_metadata/
+#> Found these file(s) with lymphgen information: METADATA_3_cohorts_lymphgen.txt
+#> # A tibble: 1,671 × 110
+#> compression bam_available patient_id sample_id seq_type capture_space
+#> <chr> <lgl> <chr> <chr> <chr> <chr>
+#> 1 bam TRUE 00-14595 00-14595_tumorA genome none
+#> 2 cram TRUE 00-14595 00-14595_tumorB genome none
+#> 3 cram TRUE 00-14595 00-14595_tumorC genome none
+#> 4 bam TRUE 00-14595 00-14595_tumorD genome none
+#> 5 cram TRUE 00-15201 00-15201_tumorA genome none
+#> 6 cram TRUE 00-15201 00-15201_tumorB genome none
+#> 7 bam TRUE 00-16220 00-16220_tumorB genome none
+#> 8 cram TRUE 00-20702 00-20702T genome none
+#> 9 cram TRUE 00-23442 00-23442_tumorA genome none
+#> 10 cram TRUE 00-23442 00-23442_tumorB genome none
+#> # ℹ 1,661 more rows
+#> # ℹ 104 more variables: genome_build <chr>, tissue_status <chr>, cohort <chr>,
+#> # library_id <chr>, pathology <chr>, time_point <chr>, protocol <chr>,
+#> # ffpe_or_frozen <chr>, read_length <dbl>, strandedness <chr>,
+#> # seq_source_type <chr>, EBV_status_inf <chr>, link_name <chr>,
+#> # data_path <chr>, unix_group <chr>, biopsy_id <chr>, fastq_link_name <chr>,
+#> # fastq_data_path <chr>, COO_consensus <chr>, DHITsig_consensus <chr>, …
#build plot
copy_number_vaf_plot(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+
#coding only
copy_number_vaf_plot(this_sample_id = "HTMCP-01-06-00422-01A-01D",
coding_only = TRUE)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+
#load a maf
this_maf = get_ssm_by_sample(this_sample_id = "HTMCP-01-06-00422-01A-01D",
this_seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#estimate purity based on an already loaded maf object
estimate_purity(maf_df = this_maf,
show_plots = TRUE)
-#> Error in dplyr::mutate(., Chromosome = gsub("chr", "", Chromosome)): object 'this_maf' not found
+#> [1] "WARNING: A seg file was not provided! Annotating all mutation calls as copy neutral"
+#> $VAF_plot
+#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
+
+#>
+#> $Purity_plot
+#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
+
+#>
+#> $sample_purity_estimation
+#> [1] 0.4471171
+#>
+#> $CN_final
+#> Hugo_Symbol Chrom_pos Chromosome Start_Position End_Position
+#> 1 TTLL10 1:1114072 1 1114072 1114072
+#> 2 ACAP3 1:1228897 1 1228897 1228897
+#> 3 PRDM16 1:3152295 1 3152295 3152295
+#> 4 Unknown 1:4047201 1 4047201 4047201
+#> 5 Unknown 1:4413966 1 4413966 4413966
+#> 6 Unknown 1:4501740 1 4501740 4501740
+#> 7 Unknown 1:5425504 1 5425504 5425504
+#> 8 Unknown 1:5788256 1 5788256 5788256
+#> 9 NPHP4 1:5970348 1 5970348 5970348
+#> 10 CAMTA1 1:7549634 1 7549634 7549634
+#> 11 RERE 1:8784688 1 8784688 8784688
+#> 12 RERE 1:8784690 1 8784690 8784706
+#> 13 Unknown 1:8914942 1 8914942 8914942
+#> 14 RP13-392I16.1 1:9564198 1 9564198 9564198
+#> 15 EXOSC10 1:11135465 1 11135465 11135465
+#> 16 VPS13D 1:12543210 1 12543210 12543210
+#> 17 Unknown 1:14323466 1 14323466 14323466
+#> 18 Unknown 1:14331526 1 14331526 14331526
+#> 19 Unknown 1:14728614 1 14728614 14728614
+#> 20 KAZN 1:15226184 1 15226184 15226184
+#> 21 KAZN 1:15315823 1 15315823 15315823
+#> 22 PADI4 1:17687332 1 17687332 17687332
+#> 23 Unknown 1:17838996 1 17838996 17838996
+#> 24 Unknown 1:18291400 1 18291400 18291400
+#> 25 IGSF21 1:18433948 1 18433948 18433948
+#> 26 IGSF21 1:18676776 1 18676776 18676776
+#> 27 ENSR00001579114 1:19291717 1 19291717 19291717
+#> 28 MINOS1 1:19921714 1 19921714 19921714
+#> 29 HP1BP3 1:21117632 1 21117632 21117632
+#> 30 RAP1GAP 1:21988253 1 21988253 21988253
+#> 31 Unknown 1:26408450 1 26408450 26408450
+#> 32 ZNF683 1:26696836 1 26696836 26696836
+#> 33 PIGV 1:27117357 1 27117357 27117357
+#> 34 PPP1R8 1:28181906 1 28181906 28181906
+#> 35 Unknown 1:29832194 1 29832194 29832194
+#> 36 Unknown 1:31060599 1 31060599 31060599
+#> 37 Unknown 1:31121775 1 31121775 31121775
+#> 38 SDC3 1:31339197 1 31339197 31339197
+#> 39 Unknown 1:31935168 1 31935168 31935168
+#> 40 SPOCD1 1:32265251 1 32265251 32265251
+#> 41 RP11-84A19.4 1:32350005 1 32350005 32350005
+#> 42 Unknown 1:33970315 1 33970315 33970315
+#> 43 CSMD2 1:34017910 1 34017910 34017910
+#> 44 CSMD2 1:34223966 1 34223966 34223966
+#> 45 AGO3 1:36423078 1 36423078 36423078
+#> 46 Unknown 1:37022782 1 37022782 37022782
+#> 47 Unknown 1:37993967 1 37993967 37993967
+#> 48 INPP5B 1:38416318 1 38416318 38416318
+#> 49 MACF1 1:39545839 1 39545839 39545839
+#> 50 KCNQ4 1:41286166 1 41286166 41286166
+#> 51 HIVEP3 1:42201533 1 42201533 42201533
+#> 52 Unknown 1:42594910 1 42594910 42594910
+#> 53 Unknown 1:43953861 1 43953861 43953861
+#> 54 RNF220 1:45050292 1 45050292 45050292
+#> 55 ZSWIM5 1:45657178 1 45657178 45657178
+#> 56 POMGNT1 1:46681699 1 46681699 46681699
+#> 57 MKNK1 1:47043611 1 47043611 47043611
+#> 58 ATPAF1 1:47131926 1 47131926 47131926
+#> 59 Unknown 1:47195243 1 47195243 47195243
+#> 60 Unknown 1:47938338 1 47938338 47938338
+#> 61 SKINTL 1:48603961 1 48603961 48603961
+#> 62 AGBL4 1:50362667 1 50362667 50362667
+#> 63 FAF1 1:50925242 1 50925242 50925242
+#> 64 FAF1 1:51105495 1 51105495 51105495
+#> 65 CALR4P 1:52038608 1 52038608 52038608
+#> 66 ZYG11A 1:53306727 1 53306727 53306727
+#> 67 CYB5RL 1:54646114 1 54646114 54646114
+#> 68 Unknown 1:54907777 1 54907777 54907777
+#> 69 Unknown 1:56365643 1 56365643 56365643
+#> 70 RP11-393I23.4 1:58550657 1 58550657 58550657
+#> 71 DAB1 1:58587493 1 58587493 58587493
+#> 72 DAB1 1:58664534 1 58664534 58664534
+#> 73 Unknown 1:60791634 1 60791634 60791634
+#> 74 INADL 1:62380515 1 62380515 62380515
+#> 75 DOCK7 1:63084997 1 63084997 63084997
+#> 76 RP11-5P4.2 1:63495858 1 63495858 63495858
+#> 77 ITGB3BP 1:64043808 1 64043808 64043808
+#> 78 UBE2U 1:64725328 1 64725328 64725328
+#> 79 Unknown 1:67928618 1 67928618 67928618
+#> 80 Unknown 1:68728818 1 68728818 68728818
+#> 81 Unknown 1:68931079 1 68931079 68931079
+#> 82 Unknown 1:69247040 1 69247040 69247040
+#> 83 Unknown 1:69272740 1 69272740 69272740
+#> 84 Unknown 1:69401231 1 69401231 69401231
+#> 85 Unknown 1:69406803 1 69406803 69406803
+#> 86 Unknown 1:69839712 1 69839712 69839712
+#> 87 ZRANB2-AS2 1:71658321 1 71658321 71658321
+#> 88 NEGR1 1:71967939 1 71967939 71967939
+#> 89 NEGR1 1:71967949 1 71967949 71967949
+#> 90 NEGR1 1:72201653 1 72201653 72201653
+#> 91 NEGR1 1:72499820 1 72499820 72499820
+#> 92 NEGR1 1:72568082 1 72568082 72568082
+#> 93 RP4-660H19.1 1:73335200 1 73335200 73335200
+#> 94 RP4-598G3.1 1:73823671 1 73823671 73823671
+#> 95 Unknown 1:73878904 1 73878904 73878913
+#> 96 LRRIQ3 1:74489187 1 74489187 74489187
+#> 97 TNNI3K 1:74929408 1 74929408 74929408
+#> 98 LRRC53 1:74959083 1 74959083 74959083
+#> 99 Unknown 1:75296628 1 75296628 75296628
+#> 100 Unknown 1:75334717 1 75334717 75334717
+#> 101 Unknown 1:75418254 1 75418254 75418254
+#> 102 MSH4 1:76281387 1 76281387 76281387
+#> 103 AK5 1:77949131 1 77949131 77949131
+#> 104 ENSR00000539381 1:78620924 1 78620924 78620924
+#> 105 Unknown 1:78677626 1 78677626 78677626
+#> 106 Unknown 1:79247413 1 79247413 79247413
+#> 107 Unknown 1:79259034 1 79259034 79259034
+#> 108 Unknown 1:79711905 1 79711905 79711905
+#> 109 Unknown 1:79717804 1 79717804 79717804
+#> 110 Unknown 1:80220310 1 80220310 80220310
+#> 111 Unknown 1:80335769 1 80335769 80335769
+#> 112 Unknown 1:80368432 1 80368432 80368432
+#> 113 RP11-339A11.1 1:80554628 1 80554628 80554628
+#> 114 Unknown 1:80653142 1 80653142 80653142
+#> 115 HMGB1P18 1:80745407 1 80745407 80745407
+#> 116 ENSR00000539596 1:81623420 1 81623420 81623445
+#> 117 LPHN2 1:81771203 1 81771203 81771203
+#> 118 LPHN2 1:81902112 1 81902112 81902112
+#> 119 Unknown 1:82559069 1 82559069 82559069
+#> 120 Unknown 1:82582645 1 82582645 82582645
+#> 121 Unknown 1:83089184 1 83089184 83089184
+#> 122 Unknown 1:83142399 1 83142399 83142399
+#> 123 RP4-601K24.1 1:83548602 1 83548602 83548602
+#> 124 Unknown 1:83641444 1 83641444 83641444
+#> 125 Unknown 1:85082968 1 85082968 85082968
+#> 126 LPAR3 1:85315342 1 85315342 85315342
+#> 127 RP4-651E10.4 1:87103687 1 87103687 87103687
+#> 128 Unknown 1:88111980 1 88111980 88111980
+#> 129 Unknown 1:88489938 1 88489938 88489938
+#> 130 Unknown 1:88816495 1 88816495 88816495
+#> 131 Unknown 1:90781971 1 90781971 90781971
+#> 132 Unknown 1:91145789 1 91145789 91145789
+#> 133 Unknown 1:91225705 1 91225705 91225705
+#> 134 BCAR3 1:94063819 1 94063819 94063819
+#> 135 RP11-286B14.1 1:95971587 1 95971587 95971587
+#> 136 Unknown 1:96279947 1 96279947 96279947
+#> 137 RP5-898J17.1 1:96725273 1 96725273 96725273
+#> 138 DPYD 1:98087658 1 98087658 98087658
+#> 139 Unknown 1:98527889 1 98527889 98527889
+#> 140 Unknown 1:99005604 1 99005604 99005604
+#> 141 Unknown 1:99300944 1 99300944 99300944
+#> 142 RP5-896L10.1 1:99587933 1 99587933 99587933
+#> 143 Unknown 1:99917820 1 99917820 99917820
+#> 144 DPH5 1:101475140 1 101475140 101475140
+#> 145 RP11-421L21.3 1:101509465 1 101509465 101509465
+#> 146 RP11-421L21.3 1:101509483 1 101509483 101509483
+#> 147 RP11-421L21.3 1:101510852 1 101510852 101510852
+#> 148 ENSR00001588509 1:101682676 1 101682676 101682678
+#> 149 RP11-411H5.1 1:102195610 1 102195610 102195610
+#> 150 OLFM3 1:102424804 1 102424804 102424804
+#> 151 Unknown 1:103162551 1 103162551 103162551
+#> 152 Unknown 1:103190564 1 103190564 103190564
+#> 153 Unknown 1:103202020 1 103202020 103202020
+#> 154 RP11-153F1.1 1:104026681 1 104026681 104026681
+#> 155 Unknown 1:104583708 1 104583708 104583708
+#> 156 Unknown 1:104733917 1 104733917 104733917
+#> 157 Unknown 1:104923941 1 104923941 104923941
+#> 158 Unknown 1:105061565 1 105061565 105061565
+#> 159 Unknown 1:105149427 1 105149427 105149427
+#> 160 Unknown 1:105385529 1 105385529 105385529
+#> 161 Unknown 1:105942423 1 105942423 105942423
+#> 162 Unknown 1:106416710 1 106416710 106416710
+#> 163 Unknown 1:106936553 1 106936553 106936553
+#> 164 RP11-478L17.1 1:107089288 1 107089288 107089288
+#> 165 AL390036.1 1:108557305 1 108557305 108557305
+#> 166 RP11-356N1.2 1:108621100 1 108621100 108621100
+#> 167 ENSR00001589110 1:110666253 1 110666253 110666253
+#> 168 CHI3L2 1:111769973 1 111769973 111769973
+#> 169 RP5-965F6.2 1:112788087 1 112788087 112788088
+#> 170 snoU13 1:112914536 1 112914536 112914536
+#> 171 CTTNBP2NL 1:112951374 1 112951374 112951374
+#> 172 ENSR00000543151 1:115951831 1 115951831 115951831
+#> 173 ENSR00000543151 1:115952023 1 115952023 115952023
+#> 174 Unknown 1:115952633 1 115952633 115952633
+#> 175 Unknown 1:118176484 1 118176484 118176484
+#> 176 ENSR00001590209 1:118213799 1 118213799 118213799
+#> 177 GDAP2 1:118443111 1 118443111 118443111
+#> 178 SPAG17 1:118691432 1 118691432 118691432
+#> 179 HSD3B1 1:120061743 1 120061743 120061743
+#> 180 RNF115 1:145664251 1 145664251 145664251
+#> 181 RNF115 1:145664823 1 145664823 145664834
+#> 182 NBPF13P 1:146594807 1 146594807 146594807
+#> 183 Unknown 1:146867820 1 146867820 146867820
+#> 184 HIST2H2AC 1:149858954 1 149858954 149858954
+#> 185 ENSR00000285690 1:150165315 1 150165315 150165315
+#> 186 FLG 1:152293199 1 152293199 152293199
+#> 187 LCE6A 1:152819154 1 152819154 152819154
+#> 188 INSRR 1:156823069 1 156823069 156823069
+#> 189 Unknown 1:159472229 1 159472229 159472229
+#> 190 Unknown 1:159600200 1 159600200 159600200
+#> 191 Unknown 1:159629761 1 159629761 159629761
+#> 192 FCRLA 1:161677403 1 161677403 161677407
+#> 193 SH2D1B 1:162360957 1 162360957 162360957
+#> 194 Unknown 1:163543178 1 163543178 163543178
+#> 195 ENSR00000546743 1:163843411 1 163843411 163843413
+#> 196 ENSR00001525494 1:163851724 1 163851724 163851724
+#> 197 PBX1 1:164724832 1 164724832 164724832
+#> 198 LMX1A 1:165279369 1 165279369 165279369
+#> 199 Unknown 1:168817856 1 168817856 168817856
+#> 200 Unknown 1:170294271 1 170294271 170294271
+#> 201 Unknown 1:170412993 1 170412993 170412993
+#> 202 RP5-1092L12.2 1:171049616 1 171049616 171049616
+#> 203 CYCSP53 1:171418921 1 171418921 171418921
+#> 204 RP1-15D23.2 1:172781009 1 172781009 172781009
+#> 205 RP1-15D23.2 1:172994673 1 172994673 172994673
+#> 206 PAPPA2 1:176531779 1 176531779 176531779
+#> 207 RP1-35C21.2 1:177368852 1 177368852 177368852
+#> 208 RP1-35C21.2 1:177404566 1 177404566 177404566
+#> 209 RP11-568K15.1 1:177976678 1 177976678 177976678
+#> 210 RP11-568K15.1 1:177976680 1 177976680 177976680
+#> 211 ENSR00000548351 1:178608097 1 178608097 178608097
+#> 212 RP11-12M5.4 1:179799444 1 179799444 179799444
+#> 213 CACNA1E 1:181659132 1 181659132 181659132
+#> 214 Unknown 1:182289113 1 182289113 182289113
+#> 215 SWT1 1:185236477 1 185236477 185236477
+#> 216 Unknown 1:187789282 1 187789282 187789282
+#> 217 Unknown 1:187823187 1 187823187 187823187
+#> 218 Unknown 1:187916721 1 187916721 187916721
+#> 219 Unknown 1:187957998 1 187957998 187957998
+#> 220 Unknown 1:188405825 1 188405825 188405825
+#> 221 LINC01035 1:188899518 1 188899518 188899518
+#> 222 Unknown 1:189410625 1 189410625 189410625
+#> 223 Unknown 1:189448825 1 189448825 189448825
+#> 224 ENSR00001527013 1:189586155 1 189586155 189586155
+#> 225 Unknown 1:189676535 1 189676535 189676535
+#> 226 Unknown 1:189929491 1 189929491 189929491
+#> 227 Unknown 1:190058991 1 190058991 190058991
+#> 228 Unknown 1:190920609 1 190920609 190920609
+#> 229 Unknown 1:191241917 1 191241917 191241917
+#> 230 Unknown 1:191394290 1 191394290 191394290
+#> 231 ENSR00000287908 1:191792375 1 191792375 191792375
+#> 232 RP11-541F9.2 1:191852739 1 191852739 191852739
+#> 233 Unknown 1:192229141 1 192229141 192229142
+#> 234 Unknown 1:193342464 1 193342464 193342464
+#> 235 RP11-563D10.1 1:194118142 1 194118142 194118142
+#> 236 Unknown 1:194374442 1 194374442 194374442
+#> 237 Unknown 1:195137478 1 195137478 195137478
+#> 238 Unknown 1:195426115 1 195426115 195426115
+#> 239 Unknown 1:195782287 1 195782287 195782287
+#> 240 KCNT2 1:196330719 1 196330719 196330719
+#> 241 KCNT2 1:196373538 1 196373538 196373538
+#> 242 CRB1 1:197269243 1 197269243 197269246
+#> 243 Unknown 1:198321772 1 198321772 198321772
+#> 244 RP11-16L9.4 1:199038729 1 199038729 199038730
+#> 245 Unknown 1:199471275 1 199471275 199471275
+#> 246 Unknown 1:199802673 1 199802673 199802673
+#> 247 TMEM9 1:201119389 1 201119389 201119389
+#> 248 NAV1 1:201651382 1 201651382 201651382
+#> 249 Unknown 1:202294435 1 202294435 202294435
+#> 250 BTG2 1:203274877 1 203274877 203274877
+#> 251 BTG2 1:203274883 1 203274883 203274883
+#> 252 BTG2 1:203275560 1 203275560 203275560
+#> 253 BTG2 1:203275563 1 203275563 203275563
+#> 254 BTG2 1:203275712 1 203275712 203275712
+#> 255 BTG2 1:203276040 1 203276040 203276040
+#> 256 BTG2 1:203276915 1 203276915 203276915
+#> 257 FAIM3 1:207093181 1 207093181 207093181
+#> 258 Unknown 1:208150605 1 208150605 208150605
+#> 259 Unknown 1:208609200 1 208609200 208609200
+#> 260 Unknown 1:209357434 1 209357434 209357434
+#> 261 HHAT 1:210503764 1 210503764 210503764
+#> 262 KCNH1 1:211065663 1 211065663 211065663
+#> 263 TRAF5 1:211503304 1 211503304 211503304
+#> 264 PPP2R5A 1:212518112 1 212518112 212518160
+#> 265 RPL31P13 1:213597631 1 213597631 213597631
+#> 266 PROX1-AS1 1:214035568 1 214035568 214035568
+#> 267 PROX1 1:214158090 1 214158090 214158090
+#> 268 Unknown 1:214287133 1 214287133 214287133
+#> 269 Unknown 1:214318476 1 214318476 214318476
+#> 270 PTPN14 1:214682615 1 214682615 214682615
+#> 271 USH2A 1:216369879 1 216369879 216369879
+#> 272 USH2A 1:216579432 1 216579432 216579432
+#> 273 ESRRG 1:216801703 1 216801703 216801705
+#> 274 LINC00210 1:218095615 1 218095615 218095615
+#> 275 Unknown 1:218177563 1 218177563 218177563
+#> 276 Unknown 1:218674605 1 218674605 218674605
+#> 277 RP11-191N8.2 1:222006358 1 222006358 222006358
+#> 278 RP11-400N13.3 1:222238518 1 222238518 222238518
+#> 279 RP11-400N13.1 1:222355739 1 222355739 222355739
+#> 280 Unknown 1:225050319 1 225050319 225050319
+#> 281 Unknown 1:226227593 1 226227593 226227593
+#> 282 PARP1 1:226595909 1 226595909 226595909
+#> 283 Unknown 1:228143738 1 228143738 228143738
+#> 284 Unknown 1:229111980 1 229111980 229111980
+#> 285 Unknown 1:229299252 1 229299252 229299252
+#> 286 Unknown 1:229304455 1 229304455 229304455
+#> 287 Unknown 1:231447248 1 231447248 231447248
+#> 288 Unknown 1:232255826 1 232255826 232255826
+#> 289 PCNXL2 1:233198061 1 233198061 233198061
+#> 290 KCNK1 1:233795126 1 233795126 233795126
+#> 291 GGPS1 1:235491917 1 235491917 235491917
+#> 292 MTR 1:237067652 1 237067652 237067652
+#> 293 RYR2 1:237449278 1 237449278 237449278
+#> 294 ZP4 1:238044992 1 238044992 238044992
+#> 295 Unknown 1:238516293 1 238516293 238516293
+#> 296 Unknown 1:238580308 1 238580308 238580308
+#> 297 Unknown 1:239151492 1 239151492 239151492
+#> 298 KIF26B 1:245422074 1 245422074 245422074
+#> 299 KIF26B 1:245725161 1 245725161 245725161
+#> 300 OR6F1 1:247876471 1 247876471 247876471
+#> 301 OR2L13 1:248122352 1 248122352 248122352
+#> 302 OR2L13 1:248252019 1 248252019 248252019
+#> 303 SH3YL1 2:214211 2 214211 214211
+#> 304 SNTG2 2:1046215 2 1046215 1046215
+#> 305 SNTG2 2:1280113 2 1280113 1280113
+#> 306 MYT1L 2:1881191 2 1881191 1881191
+#> 307 Unknown 2:2423956 2 2423956 2423956
+#> 308 Unknown 2:5711406 2 5711406 5711406
+#> 309 Unknown 2:6220275 2 6220275 6220275
+#> 310 Unknown 2:6557656 2 6557656 6557656
+#> 311 Unknown 2:7249110 2 7249110 7249110
+#> 312 LINC00299 2:8516942 2 8516942 8516942
+#> 313 LPIN1 2:11894233 2 11894233 11894233
+#> 314 AC096559.1 2:12434172 2 12434172 12434172
+#> 315 Unknown 2:13655806 2 13655806 13655806
+#> 316 Unknown 2:14644128 2 14644128 14644128
+#> 317 Unknown 2:16478047 2 16478047 16478047
+#> 318 Unknown 2:17435658 2 17435658 17435658
+#> 319 PUM2 2:20446016 2 20446016 20446016
+#> 320 C2orf43 2:20966254 2 20966254 20966254
+#> 321 AC067959.1 2:22077729 2 22077729 22077729
+#> 322 AC068490.2 2:22216304 2 22216304 22216304
+#> 323 AC068490.2 2:22547497 2 22547497 22547497
+#> 324 Unknown 2:23044015 2 23044015 23044015
+#> 325 Unknown 2:23073787 2 23073787 23073787
+#> 326 ALK 2:29470202 2 29470202 29470203
+#> 327 ALK 2:29659592 2 29659592 29659592
+#> 328 Unknown 2:30259816 2 30259816 30259816
+#> 329 AL133247.3 2:31875558 2 31875558 31875558
+#> 330 LTBP1 2:33262348 2 33262348 33262348
+#> 331 AC009499.1 2:34509415 2 34509415 34509415
+#> 332 AC012593.1 2:35405237 2 35405237 35405237
+#> 333 Unknown 2:35751779 2 35751779 35751779
+#> 334 Unknown 2:36338829 2 36338829 36338829
+#> 335 ARHGEF33 2:39131026 2 39131026 39131026
+#> 336 SLC8A1-AS1 2:40173833 2 40173833 40173833
+#> 337 SLC8A1 2:40351922 2 40351922 40351922
+#> 338 SLC8A1 2:40394184 2 40394184 40394184
+#> 339 Unknown 2:40955465 2 40955465 40955465
+#> 340 Unknown 2:41099628 2 41099628 41099628
+#> 341 Unknown 2:41192419 2 41192419 41192420
+#> 342 AC098824.6 2:43058486 2 43058486 43058486
+#> 343 LINC01121 2:45496631 2 45496631 45496631
+#> 344 C2orf61 2:47337349 2 47337349 47337349
+#> 345 Unknown 2:48142306 2 48142306 48142306
+#> 346 Unknown 2:49649829 2 49649829 49649829
+#> 347 AC007682.1 2:51755509 2 51755509 51755510
+#> 348 AC007682.1 2:51964663 2 51964663 51964663
+#> 349 AC007682.1 2:51978267 2 51978267 51978267
+#> 350 AC007682.1 2:52024003 2 52024003 52024003
+#> 351 AC007682.1 2:52306947 2 52306947 52306947
+#> 352 Unknown 2:53346604 2 53346604 53346604
+#> 353 PSME4 2:54139805 2 54139805 54139805
+#> 354 CCDC88A 2:55635068 2 55635068 55635068
+#> 355 RP11-481J13.1 2:56288504 2 56288504 56288504
+#> 356 LINC01122 2:59213574 2 59213574 59213574
+#> 357 Unknown 2:59383381 2 59383381 59383381
+#> 358 RP11-444A22.1 2:59948873 2 59948873 59948873
+#> 359 Unknown 2:60568906 2 60568906 60568906
+#> 360 BCL11A 2:60779372 2 60779372 60779372
+#> 361 KIAA1841 2:61307862 2 61307862 61307862
+#> 362 AC016727.3 2:61818144 2 61818144 61818144
+#> 363 CCT4 2:62106055 2 62106055 62106055
+#> 364 Unknown 2:62666432 2 62666432 62666432
+#> 365 AC092155.1 2:62759500 2 62759500 62759500
+#> 366 PSAT1P2 2:62777920 2 62777920 62777920
+#> 367 ENSR00000591568 2:64501657 2 64501657 64501657
+#> 368 AC074391.1 2:66288568 2 66288568 66288568
+#> 369 AC074391.1 2:66308795 2 66308795 66308795
+#> 370 Unknown 2:67029204 2 67029204 67029204
+#> 371 AC078941.1 2:67398985 2 67398985 67398985
+#> 372 ENSR00000013746 2:68067986 2 68067986 68067986
+#> 373 WDR92 2:68379894 2 68379894 68379894
+#> 374 ANTXR1 2:69332078 2 69332078 69332078
+#> 375 FIGLA 2:71011065 2 71011065 71011065
+#> 376 EXOC6B 2:72490872 2 72490872 72490872
+#> 377 ALMS1 2:73631253 2 73631253 73631253
+#> 378 TPRKB 2:73963710 2 73963710 73963710
+#> 379 Unknown 2:76047044 2 76047044 76047044
+#> 380 Unknown 2:76590356 2 76590356 76590356
+#> 381 LRRTM4 2:77182723 2 77182723 77182723
+#> 382 LRRTM4 2:77558401 2 77558401 77558401
+#> 383 LRRTM4 2:77677597 2 77677597 77677597
+#> 384 Unknown 2:77977154 2 77977154 77977154
+#> 385 AC105399.2 2:78015118 2 78015118 78015118
+#> 386 Unknown 2:78041337 2 78041337 78041337
+#> 387 Unknown 2:78515302 2 78515302 78515302
+#> 388 Unknown 2:78624645 2 78624645 78624645
+#> 389 Unknown 2:78720870 2 78720870 78720870
+#> 390 ENSR00000676709 2:78900418 2 78900418 78900418
+#> 391 Unknown 2:78987994 2 78987994 78987994
+#> 392 Unknown 2:79032787 2 79032787 79032787
+#> 393 CTNNA2 2:79726999 2 79726999 79726999
+#> 394 CTNNA2 2:80188843 2 80188843 80188843
+#> 395 CTNNA2 2:80754827 2 80754827 80754827
+#> 396 CTNNA2 2:80835537 2 80835537 80835537
+#> 397 AC084193.1 2:81007847 2 81007847 81007847
+#> 398 Unknown 2:81285239 2 81285239 81285239
+#> 399 Unknown 2:81599558 2 81599558 81599558
+#> 400 Unknown 2:81628268 2 81628268 81628268
+#> 401 Unknown 2:81996827 2 81996827 81996827
+#> 402 AC079896.1 2:82218340 2 82218340 82218340
+#> 403 AC079896.1 2:82218345 2 82218345 82218345
+#> 404 AC079896.1 2:82223449 2 82223449 82223449
+#> 405 Unknown 2:82310140 2 82310140 82310140
+#> 406 Unknown 2:82622351 2 82622351 82622351
+#> 407 AC010105.1 2:82736109 2 82736109 82736109
+#> 408 Unknown 2:82897464 2 82897464 82897464
+#> 409 Unknown 2:83111707 2 83111707 83111707
+#> 410 Unknown 2:83312941 2 83312941 83312941
+#> 411 Unknown 2:83440307 2 83440307 83440307
+#> 412 Unknown 2:83735456 2 83735456 83735456
+#> 413 Unknown 2:84054444 2 84054444 84054444
+#> 414 Unknown 2:95435473 2 95435473 95435473
+#> 415 DUSP2 2:96809892 2 96809892 96809892
+#> 416 INPP4A 2:99059138 2 99059138 99059138
+#> 417 AFF3 2:100757910 2 100757910 100757917
+#> 418 ENSR00001544749 2:101368077 2 101368077 101368077
+#> 419 Unknown 2:103809888 2 103809888 103809888
+#> 420 Unknown 2:104090590 2 104090590 104090590
+#> 421 Unknown 2:104292165 2 104292165 104292165
+#> 422 Unknown 2:104841245 2 104841245 104841245
+#> 423 Unknown 2:105242159 2 105242159 105242159
+#> 424 Unknown 2:106673304 2 106673304 106673304
+#> 425 UXS1 2:106808220 2 106808220 106808220
+#> 426 Unknown 2:106951433 2 106951433 106951433
+#> 427 Unknown 2:107384809 2 107384809 107384809
+#> 428 ST6GAL2 2:107496677 2 107496677 107496677
+#> 429 AC096669.2 2:108027636 2 108027636 108027636
+#> 430 GACAT1 2:108409109 2 108409109 108409109
+#> 431 Unknown 2:108596843 2 108596843 108596843
+#> 432 Unknown 2:108596875 2 108596875 108596875
+#> 433 SULT1C3 2:108875923 2 108875923 108875923
+#> 434 SH3RF3 2:109817612 2 109817612 109817612
+#> 435 MERTK 2:112679811 2 112679811 112679811
+#> 436 DPP10 2:115919819 2 115919819 115919819
+#> 437 DPP10 2:115955476 2 115955476 115955476
+#> 438 DPP10 2:116006461 2 116006461 116006471
+#> 439 DPP10 2:116481654 2 116481654 116481654
+#> 440 Unknown 2:116796278 2 116796278 116796278
+#> 441 Unknown 2:116942293 2 116942293 116942293
+#> 442 Unknown 2:117020369 2 117020369 117020369
+#> 443 Unknown 2:117096314 2 117096314 117096314
+#> 444 Unknown 2:117131393 2 117131393 117131393
+#> 445 Unknown 2:117181645 2 117181645 117181645
+#> 446 Unknown 2:117533342 2 117533342 117533342
+#> 447 Unknown 2:117803253 2 117803253 117803253
+#> 448 Unknown 2:117864780 2 117864780 117864780
+#> 449 Unknown 2:118104627 2 118104627 118104627
+#> 450 Unknown 2:118334848 2 118334848 118334848
+#> 451 Unknown 2:119368363 2 119368363 119368363
+#> 452 Unknown 2:119615864 2 119615864 119615864
+#> 453 Unknown 2:119764371 2 119764371 119764371
+#> 454 Unknown 2:121417517 2 121417517 121417517
+#> 455 Unknown 2:122603193 2 122603193 122603193
+#> 456 Unknown 2:123685854 2 123685854 123685854
+#> 457 Unknown 2:123816596 2 123816596 123816596
+#> 458 Unknown 2:123874476 2 123874476 123874476
+#> 459 Unknown 2:124508060 2 124508060 124508060
+#> 460 CNTNAP5 2:124813880 2 124813880 124813880
+#> 461 Unknown 2:125762409 2 125762409 125762410
+#> 462 Unknown 2:125788468 2 125788468 125788468
+#> 463 Unknown 2:125828925 2 125828925 125828925
+#> 464 Unknown 2:125851087 2 125851087 125851087
+#> 465 Unknown 2:126323575 2 126323575 126323575
+#> 466 Unknown 2:126350465 2 126350465 126350465
+#> 467 Unknown 2:126361628 2 126361628 126361628
+#> 468 Unknown 2:126382452 2 126382452 126382452
+#> 469 Unknown 2:126442719 2 126442719 126442719
+#> 470 Unknown 2:127766297 2 127766297 127766297
+#> 471 Unknown 2:129125733 2 129125733 129125733
+#> 472 GPR39 2:133246782 2 133246782 133246782
+#> 473 NCKAP5 2:134027992 2 134027992 134027992
+#> 474 Unknown 2:134593042 2 134593042 134593042
+#> 475 CCNT2 2:135690560 2 135690560 135690560
+#> 476 HNRNPKP2 2:136961969 2 136961969 136961969
+#> 477 Unknown 2:138821997 2 138821997 138821997
+#> 478 NXPH2 2:139482652 2 139482652 139482652
+#> 479 Unknown 2:140345911 2 140345911 140345911
+#> 480 Unknown 2:140504529 2 140504529 140504529
+#> 481 Unknown 2:140788063 2 140788063 140788063
+#> 482 Unknown 2:140813458 2 140813458 140813458
+#> 483 Unknown 2:140825990 2 140825990 140825990
+#> 484 LRP1B 2:141046040 2 141046040 141046040
+#> 485 LRP1B 2:141509525 2 141509525 141509525
+#> 486 LRP1B 2:142078076 2 142078076 142078076
+#> 487 LRP1B 2:142206019 2 142206019 142206019
+#> 488 Unknown 2:143357019 2 143357019 143357019
+#> 489 Unknown 2:144546859 2 144546859 144546859
+#> 490 Unknown 2:146869433 2 146869433 146869433
+#> 491 MBD5 2:149036378 2 149036378 149036378
+#> 492 KIF5C 2:149828098 2 149828098 149828098
+#> 493 Unknown 2:150392100 2 150392100 150392100
+#> 494 Unknown 2:151709663 2 151709663 151709663
+#> 495 Unknown 2:153876234 2 153876234 153876234
+#> 496 RPRM 2:154336778 2 154336778 154336778
+#> 497 GALNT13 2:155305426 2 155305426 155305426
+#> 498 Unknown 2:155815682 2 155815682 155815682
+#> 499 Unknown 2:155878422 2 155878422 155878422
+#> 500 Unknown 2:156157416 2 156157416 156157416
+#> 501 ACVR1 2:158693126 2 158693126 158693126
+#> 502 UPP2 2:158855742 2 158855742 158855742
+#> 503 BAZ2B 2:160191404 2 160191404 160191405
+#> 504 BAZ2B 2:160292505 2 160292505 160292505
+#> 505 KCNH7 2:163339793 2 163339793 163339793
+#> 506 KCNH7 2:163693132 2 163693132 163693132
+#> 507 Unknown 2:163967106 2 163967106 163967106
+#> 508 Unknown 2:164411238 2 164411238 164411238
+#> 509 SCN2A 2:166124099 2 166124099 166124099
+#> 510 SCN2A 2:166180970 2 166180970 166180970
+#> 511 CSRNP3 2:166327852 2 166327852 166327852
+#> 512 AC010127.3 2:166942931 2 166942931 166942931
+#> 513 AC016723.4 2:168779782 2 168779782 168779782
+#> 514 UBE2V1P6 2:169968887 2 169968887 169968887
+#> 515 METTL5 2:170679766 2 170679766 170679766
+#> 516 Unknown 2:173159674 2 173159674 173159674
+#> 517 RP11-324L17.1 2:177476603 2 177476603 177476603
+#> 518 Unknown 2:181399104 2 181399104 181399104
+#> 519 ITGA4 2:182379656 2 182379656 182379656
+#> 520 Unknown 2:183427760 2 183427760 183427760
+#> 521 Unknown 2:183748174 2 183748174 183748174
+#> 522 Unknown 2:184866266 2 184866266 184866266
+#> 523 Unknown 2:185023211 2 185023211 185023211
+#> 524 Unknown 2:185071735 2 185071735 185071735
+#> 525 FSIP2 2:186647052 2 186647052 186647052
+#> 526 Unknown 2:186784590 2 186784590 186784590
+#> 527 Unknown 2:187022223 2 187022223 187022223
+#> 528 ITGAV 2:187484243 2 187484243 187484243
+#> 529 CALCRL 2:188231118 2 188231118 188231118
+#> 530 LINC01090 2:188587938 2 188587938 188587938
+#> 531 LINC01090 2:188663287 2 188663287 188663287
+#> 532 GULP1 2:189202276 2 189202276 189202276
+#> 533 AC079613.1 2:189541642 2 189541642 189541642
+#> 534 ANKAR 2:190550847 2 190550847 190550847
+#> 535 C2orf88 2:191022188 2 191022188 191022188
+#> 536 Unknown 2:192073352 2 192073352 192073354
+#> 537 TMEFF2 2:192887521 2 192887521 192887521
+#> 538 TMEFF2 2:192954570 2 192954570 192954570
+#> 539 Unknown 2:193954247 2 193954247 193954247
+#> 540 Unknown 2:194111032 2 194111032 194111032
+#> 541 Unknown 2:194417969 2 194417969 194417969
+#> 542 Unknown 2:194839825 2 194839825 194839825
+#> 543 Unknown 2:195082956 2 195082956 195082956
+#> 544 DNAH7 2:196663624 2 196663624 196663624
+#> 545 AC019330.1 2:199531075 2 199531075 199531075
+#> 546 Unknown 2:199693993 2 199693993 199693993
+#> 547 Unknown 2:200043124 2 200043124 200043124
+#> 548 ALS2CR11 2:202480914 2 202480914 202480914
+#> 549 ALS2 2:202564280 2 202564280 202564280
+#> 550 Unknown 2:202889656 2 202889656 202889656
+#> 551 AC009498.1 2:205099214 2 205099214 205099214
+#> 552 PARD3B 2:205520281 2 205520281 205520281
+#> 553 PARD3B 2:206032506 2 206032506 206032506
+#> 554 PARD3B 2:206270665 2 206270665 206270665
+#> 555 HNRNPA1P51 2:207280535 2 207280535 207280535
+#> 556 CCNYL1 2:208595166 2 208595166 208595166
+#> 557 ENSR00001551139 2:208649988 2 208649988 208649988
+#> 558 CRYGEP 2:208978089 2 208978089 208978089
+#> 559 PTH2R 2:209268597 2 209268597 209268597
+#> 560 PTH2R 2:209336696 2 209336696 209336696
+#> 561 PTH2R 2:209487152 2 209487152 209487152
+#> 562 MAP2 2:210515725 2 210515725 210515725
+#> 563 CPS1 2:211496612 2 211496612 211496612
+#> 564 Unknown 2:211665187 2 211665187 211665187
+#> 565 ERBB4 2:212488881 2 212488881 212488881
+#> 566 ERBB4 2:212840926 2 212840926 212840926
+#> 567 ERBB4 2:213259023 2 213259023 213259023
+#> 568 ERBB4 2:213301284 2 213301284 213301284
+#> 569 AC079610.1 2:213596674 2 213596674 213596674
+#> 570 AC079610.1 2:213608363 2 213608363 213608363
+#> 571 AC079610.1 2:213736031 2 213736031 213736031
+#> 572 IKZF2 2:213941598 2 213941598 213941598
+#> 573 SPAG16 2:214750425 2 214750425 214750425
+#> 574 AC107218.3 2:215544758 2 215544758 215544758
+#> 575 LINC00607 2:216629389 2 216629389 216629389
+#> 576 MARCH4 2:217232624 2 217232624 217232624
+#> 577 AC098820.2 2:217267373 2 217267373 217267373
+#> 578 AC007563.5 2:217852805 2 217852805 217852805
+#> 579 AC114765.1 2:221063826 2 221063826 221063826
+#> 580 AC114765.1 2:221206991 2 221206991 221206991
+#> 581 AC067956.1 2:221369474 2 221369474 221369474
+#> 582 AC067956.1 2:221369482 2 221369482 221369482
+#> 583 AC067956.1 2:221551046 2 221551046 221551046
+#> 584 Unknown 2:221936047 2 221936047 221936047
+#> 585 Unknown 2:222172297 2 222172297 222172297
+#> 586 Unknown 2:222215062 2 222215062 222215062
+#> 587 ENSR00001715527 2:222265277 2 222265277 222265277
+#> 588 EPHA4 2:222303647 2 222303647 222303647
+#> 589 AC079834.1 2:222458134 2 222458134 222458134
+#> 590 MOGAT1 2:223550183 2 223550183 223550183
+#> 591 KCNE4 2:224043108 2 224043108 224043108
+#> 592 Unknown 2:224237058 2 224237058 224237058
+#> 593 Unknown 2:225182158 2 225182158 225182158
+#> 594 NYAP2 2:226438098 2 226438098 226438098
+#> 595 Unknown 2:226951407 2 226951407 226951407
+#> 596 Unknown 2:227405974 2 227405974 227405974
+#> 597 Unknown 2:229267842 2 229267842 229267842
+#> 598 AC009410.1 2:229357962 2 229357962 229357962
+#> 599 AC009410.1 2:229406274 2 229406274 229406274
+#> 600 PID1 2:229832607 2 229832607 229832607
+#> 601 ARMC9 2:232238808 2 232238808 232238808
+#> 602 INPP5D 2:233965600 2 233965600 233965600
+#> 603 Unknown 2:235633609 2 235633609 235633609
+#> 604 AGAP1 2:236941867 2 236941867 236941867
+#> 605 AC113618.1 2:239641879 2 239641879 239641879
+#> 606 HDAC4 2:240174822 2 240174822 240174822
+#> 607 Unknown 2:240447361 2 240447361 240447361
+#> 608 Unknown 2:242776518 2 242776518 242776518
+#> 609 CHL1 3:327229 3 327229 327229
+#> 610 Unknown 3:1799265 3 1799265 1799265
+#> 611 Unknown 3:1831099 3 1831099 1831099
+#> 612 CNTN4 3:2552893 3 2552893 2552893
+#> 613 CNTN4 3:3029421 3 3029421 3029421
+#> 614 AC026188.1 3:3468987 3 3468987 3468987
+#> 615 Unknown 3:5835834 3 5835834 5835834
+#> 616 Unknown 3:6478173 3 6478173 6478173
+#> 617 GRM7 3:6859198 3 6859198 6859198
+#> 618 GRM7 3:6917171 3 6917171 6917171
+#> 619 GRM7 3:6991321 3 6991321 6991321
+#> 620 GRM7 3:7201092 3 7201092 7201092
+#> 621 GRM7 3:7737633 3 7737633 7737633
+#> 622 Unknown 3:10848288 3 10848288 10848288
+#> 623 SLC6A1 3:11037883 3 11037883 11037883
+#> 624 ENSR00001476539 3:11158507 3 11158507 11158507
+#> 625 ATG7 3:11592799 3 11592799 11592799
+#> 626 VGLL4 3:11643615 3 11643615 11643615
+#> 627 RPL32 3:12882370 3 12882370 12882370
+#> 628 WNT7A 3:13903691 3 13903691 13903691
+#> 629 C3orf20 3:14799275 3 14799275 14799275
+#> 630 OXNAD1 3:16322700 3 16322700 16322700
+#> 631 DAZL 3:16685168 3 16685168 16685168
+#> 632 TBC1D5 3:18046907 3 18046907 18046907
+#> 633 AC144521.1 3:18947298 3 18947298 18947298
+#> 634 Unknown 3:19751404 3 19751404 19751404
+#> 635 Unknown 3:20333686 3 20333686 20333686
+#> 636 Unknown 3:20467221 3 20467221 20467221
+#> 637 Unknown 3:21344050 3 21344050 21344050
+#> 638 Unknown 3:21391586 3 21391586 21391586
+#> 639 ZNF385D 3:21730420 3 21730420 21730420
+#> 640 ZNF385D 3:21747628 3 21747628 21747628
+#> 641 ZNF385D 3:21830776 3 21830776 21830776
+#> 642 ZNF385D 3:21958110 3 21958110 21958115
+#> 643 ZNF385D 3:22222758 3 22222758 22222758
+#> 644 ZNF385D 3:22288293 3 22288293 22288294
+#> 645 Unknown 3:22559006 3 22559006 22559006
+#> 646 Unknown 3:22810755 3 22810755 22810755
+#> 647 ENSR00001737154 3:23689086 3 23689086 23689086
+#> 648 ENSR00001359446 3:24045942 3 24045942 24045942
+#> 649 THRB 3:24366941 3 24366941 24366941
+#> 650 THRB 3:24436696 3 24436696 24436696
+#> 651 AC133680.1 3:25130763 3 25130763 25130763
+#> 652 Unknown 3:26031602 3 26031602 26031602
+#> 653 Unknown 3:26306558 3 26306558 26306558
+#> 654 Unknown 3:26397365 3 26397365 26397365
+#> 655 Unknown 3:26475705 3 26475705 26475705
+#> 656 Unknown 3:26508896 3 26508896 26508896
+#> 657 Unknown 3:26942988 3 26942988 26942988
+#> 658 NEK10 3:27162961 3 27162961 27162961
+#> 659 NEK10 3:27324389 3 27324389 27324389
+#> 660 Unknown 3:28244616 3 28244616 28244616
+#> 661 ZCWPW2 3:28444889 3 28444889 28444889
+#> 662 Unknown 3:28972642 3 28972642 28972642
+#> 663 Unknown 3:29074226 3 29074226 29074226
+#> 664 RBMS3 3:29731706 3 29731706 29731706
+#> 665 RBMS3 3:29921843 3 29921843 29921843
+#> 666 RBMS3 3:30012598 3 30012598 30012598
+#> 667 TGFBR2 3:30650535 3 30650535 30650535
+#> 668 AC104306.2 3:32553997 3 32553997 32553997
+#> 669 Unknown 3:33284376 3 33284376 33284376
+#> 670 Unknown 3:33313095 3 33313095 33313095
+#> 671 Unknown 3:33965412 3 33965412 33965412
+#> 672 AC018359.1 3:34253545 3 34253545 34253545
+#> 673 AC018359.1 3:34339722 3 34339722 34339722
+#> 674 AC018359.1 3:34466334 3 34466334 34466334
+#> 675 Unknown 3:34640209 3 34640209 34640209
+#> 676 Unknown 3:34686291 3 34686291 34686291
+#> 677 Unknown 3:34712764 3 34712764 34712764
+#> 678 Unknown 3:35069783 3 35069783 35069783
+#> 679 Unknown 3:35573122 3 35573122 35573122
+#> 680 Unknown 3:36272730 3 36272730 36272730
+#> 681 GOLGA4 3:37339381 3 37339381 37339381
+#> 682 MOBP 3:39543808 3 39543808 39543808
+#> 683 Unknown 3:39650101 3 39650101 39650101
+#> 684 ENTPD3 3:40474506 3 40474506 40474506
+#> 685 RP11-528N21.1 3:40648794 3 40648794 40648794
+#> 686 Unknown 3:42391710 3 42391710 42391710
+#> 687 ANO10 3:43510069 3 43510069 43510069
+#> 688 CDCP1 3:45177407 3 45177407 45177407
+#> 689 SLC6A20 3:45803989 3 45803989 45803989
+#> 690 ENSR00001478820 3:46166888 3 46166888 46166889
+#> 691 SMARCC1 3:47684241 3 47684241 47684241
+#> 692 SMARCC1 3:47702636 3 47702636 47702636
+#> 693 ZNF589 3:48316150 3 48316150 48316150
+#> 694 BSN 3:49626878 3 49626878 49626878
+#> 695 DOCK3 3:50880083 3 50880083 50880083
+#> 696 DOCK3 3:51321486 3 51321486 51321486
+#> 697 Unknown 3:52062223 3 52062223 52062223
+#> 698 DNAH1 3:52357578 3 52357578 52357578
+#> 699 Unknown 3:54107097 3 54107097 54107097
+#> 700 CACNA2D3 3:54544369 3 54544369 54544369
+#> 701 CACNA2D3 3:54841378 3 54841378 54841378
+#> 702 CACNA2D3 3:55027230 3 55027230 55027230
+#> 703 Unknown 3:55195166 3 55195166 55195166
+#> 704 RP11-875H7.2 3:55392301 3 55392301 55392301
+#> 705 ERC2 3:55597773 3 55597773 55597773
+#> 706 Unknown 3:56521482 3 56521482 56521482
+#> 707 Unknown 3:56744842 3 56744842 56744842
+#> 708 C3orf67 3:58932722 3 58932722 58932722
+#> 709 C3orf67 3:58960160 3 58960160 58960160
+#> 710 Unknown 3:59295675 3 59295675 59295675
+#> 711 FHIT 3:60036543 3 60036543 60036546
+#> 712 FHIT 3:60109988 3 60109988 60109988
+#> 713 FHIT 3:60701603 3 60701603 60701603
+#> 714 Unknown 3:61389814 3 61389814 61389814
+#> 715 PTPRG 3:61608735 3 61608735 61608735
+#> 716 PTPRG 3:61925780 3 61925780 61925780
+#> 717 PTPRG 3:62022653 3 62022653 62022653
+#> 718 AC136289.1 3:63791205 3 63791205 63791205
+#> 719 PRICKLE2 3:64324378 3 64324378 64324378
+#> 720 MAGI1 3:65401976 3 65401976 65401976
+#> 721 MAGI1 3:65406424 3 65406424 65406424
+#> 722 SLC25A26 3:66286503 3 66286503 66286503
+#> 723 RP11-81N13.1 3:67822149 3 67822149 67822149
+#> 724 Unknown 3:68024548 3 68024548 68024549
+#> 725 FAM19A1 3:68344838 3 68344838 68344838
+#> 726 FAM19A1 3:68418026 3 68418026 68418026
+#> 727 FAM19A1 3:68439563 3 68439563 68439563
+#> 728 FRMD4B 3:69324639 3 69324639 69324639
+#> 729 FRMD4B 3:69330924 3 69330924 69330924
+#> 730 RP11-62G11.2 3:69610702 3 69610702 69610702
+#> 731 MITF 3:69842373 3 69842373 69842373
+#> 732 MITF 3:69922293 3 69922293 69922293
+#> 733 FOXP1 3:71150016 3 71150016 71150016
+#> 734 FOXP1 3:71178979 3 71178979 71178979
+#> 735 FOXP1 3:71183947 3 71183947 71183947
+#> 736 LINC00877 3:72160564 3 72160564 72160564
+#> 737 RYBP 3:72446051 3 72446051 72446051
+#> 738 Unknown 3:72609802 3 72609802 72609802
+#> 739 PDZRN3 3:73459852 3 73459852 73459852
+#> 740 CNTN3 3:74359226 3 74359226 74359226
+#> 741 CNTN3 3:74398955 3 74398955 74398955
+#> 742 CNTN3 3:74409925 3 74409925 74409925
+#> 743 Unknown 3:74657360 3 74657360 74657360
+#> 744 Unknown 3:74753744 3 74753744 74753744
+#> 745 Unknown 3:74842709 3 74842709 74842709
+#> 746 Unknown 3:74862840 3 74862840 74862840
+#> 747 Unknown 3:75272964 3 75272964 75272964
+#> 748 Unknown 3:75339336 3 75339336 75339336
+#> 749 FAM86DP 3:75470357 3 75470357 75470357
+#> 750 ROBO2 3:76139752 3 76139752 76139752
+#> 751 ROBO2 3:76167920 3 76167920 76167920
+#> 752 ROBO2 3:76180479 3 76180479 76180479
+#> 753 ROBO2 3:76212324 3 76212324 76212324
+#> 754 ROBO2 3:76421841 3 76421841 76421841
+#> 755 ROBO2 3:76496065 3 76496065 76496065
+#> 756 ROBO2 3:76595721 3 76595721 76595721
+#> 757 ROBO2 3:76713958 3 76713958 76713958
+#> 758 ROBO2 3:76759381 3 76759381 76759381
+#> 759 ROBO2 3:76820290 3 76820290 76820290
+#> 760 ROBO2 3:76996001 3 76996001 76996001
+#> 761 ROBO2 3:77033537 3 77033537 77033538
+#> 762 ROBO2 3:77091452 3 77091452 77091452
+#> 763 ROBO2 3:77168424 3 77168424 77168424
+#> 764 ROBO2 3:77296013 3 77296013 77296013
+#> 765 ROBO2 3:77614639 3 77614639 77614639
+#> 766 ROBO2 3:77625008 3 77625008 77625008
+#> 767 Unknown 3:78036812 3 78036812 78036812
+#> 768 Unknown 3:78262304 3 78262304 78262304
+#> 769 Unknown 3:78374366 3 78374366 78374366
+#> t_ref_count t_alt_count CN VAF Ploidy Purity CCF_mutation
+#> 1 61 33 2 0.35106383 1 0.7021277 0.6820669
+#> 2 63 21 2 0.25000000 1 0.5000000 0.4857143
+#> 3 50 19 2 0.27536232 1 0.5507246 0.5349896
+#> 4 78 16 2 0.17021277 1 0.3404255 0.3306991
+#> 5 60 15 2 0.20000000 1 0.4000000 0.3885714
+#> 6 71 16 2 0.18390805 1 0.3678161 0.3573071
+#> 7 67 15 2 0.18292683 1 0.3658537 0.3554007
+#> 8 59 19 2 0.24358974 1 0.4871795 0.4732601
+#> 9 56 18 2 0.24324324 1 0.4864865 0.4725869
+#> 10 73 14 2 0.16091954 1 0.3218391 0.3126437
+#> 11 43 9 2 0.17307692 1 0.3461538 0.3362637
+#> 12 48 9 2 0.15789474 1 0.3157895 0.3067669
+#> 13 58 15 2 0.20547945 1 0.4109589 0.3992172
+#> 14 60 14 2 0.18918919 1 0.3783784 0.3675676
+#> 15 59 23 2 0.28048780 1 0.5609756 0.5449477
+#> 16 59 17 2 0.22368421 1 0.4473684 0.4345865
+#> 17 62 28 2 0.31111111 1 0.6222222 0.6044444
+#> 18 77 17 2 0.18085106 1 0.3617021 0.3513678
+#> 19 65 15 2 0.18750000 1 0.3750000 0.3642857
+#> 20 44 18 2 0.29032258 1 0.5806452 0.5640553
+#> 21 59 12 2 0.16901408 1 0.3380282 0.3283702
+#> 22 50 15 2 0.23076923 1 0.4615385 0.4483516
+#> 23 50 16 2 0.24242424 1 0.4848485 0.4709957
+#> 24 63 10 2 0.13698630 1 0.2739726 0.2661448
+#> 25 50 15 2 0.23076923 1 0.4615385 0.4483516
+#> 26 59 17 2 0.22368421 1 0.4473684 0.4345865
+#> 27 65 20 2 0.23529412 1 0.4705882 0.4571429
+#> 28 80 9 2 0.10112360 1 0.2022472 0.1964687
+#> 29 61 18 2 0.22784810 1 0.4556962 0.4426763
+#> 30 61 21 2 0.25609756 1 0.5121951 0.4975610
+#> 31 53 16 2 0.23188406 1 0.4637681 0.4505176
+#> 32 66 18 2 0.21428571 1 0.4285714 0.4163265
+#> 33 64 23 2 0.26436782 1 0.5287356 0.5136289
+#> 34 63 15 2 0.19230769 1 0.3846154 0.3736264
+#> 35 65 25 2 0.27777778 1 0.5555556 0.5396825
+#> 36 61 15 2 0.19736842 1 0.3947368 0.3834586
+#> 37 57 18 2 0.24000000 1 0.4800000 0.4662857
+#> 38 72 14 2 0.16279070 1 0.3255814 0.3162791
+#> 39 62 19 2 0.23456790 1 0.4691358 0.4557319
+#> 40 79 20 2 0.20202020 1 0.4040404 0.3924964
+#> 41 50 16 2 0.24242424 1 0.4848485 0.4709957
+#> 42 75 19 2 0.20212766 1 0.4042553 0.3927052
+#> 43 55 17 2 0.23611111 1 0.4722222 0.4587302
+#> 44 59 18 2 0.23376623 1 0.4675325 0.4541744
+#> 45 63 16 2 0.20253165 1 0.4050633 0.3934901
+#> 46 61 27 2 0.30681818 1 0.6136364 0.5961039
+#> 47 47 15 2 0.24193548 1 0.4838710 0.4700461
+#> 48 45 17 2 0.27419355 1 0.5483871 0.5327189
+#> 49 58 19 2 0.24675325 1 0.4935065 0.4794063
+#> 50 50 21 2 0.29577465 1 0.5915493 0.5746479
+#> 51 60 16 2 0.21052632 1 0.4210526 0.4090226
+#> 52 61 18 2 0.22784810 1 0.4556962 0.4426763
+#> 53 47 19 2 0.28787879 1 0.5757576 0.5593074
+#> 54 69 14 2 0.16867470 1 0.3373494 0.3277108
+#> 55 72 9 2 0.11111111 1 0.2222222 0.2158730
+#> 56 30 9 2 0.23076923 1 0.4615385 0.4483516
+#> 57 58 18 2 0.23684211 1 0.4736842 0.4601504
+#> 58 60 15 2 0.20000000 1 0.4000000 0.3885714
+#> 59 61 22 2 0.26506024 1 0.5301205 0.5149742
+#> 60 44 19 2 0.30158730 1 0.6031746 0.5859410
+#> 61 49 18 2 0.26865672 1 0.5373134 0.5219616
+#> 62 49 13 2 0.20967742 1 0.4193548 0.4073733
+#> 63 53 20 2 0.27397260 1 0.5479452 0.5322896
+#> 64 49 13 2 0.20967742 1 0.4193548 0.4073733
+#> 65 56 20 2 0.26315789 1 0.5263158 0.5112782
+#> 66 71 15 2 0.17441860 1 0.3488372 0.3388704
+#> 67 48 19 2 0.28358209 1 0.5671642 0.5509595
+#> 68 61 23 2 0.27380952 1 0.5476190 0.5319728
+#> 69 63 10 2 0.13698630 1 0.2739726 0.2661448
+#> 70 54 23 2 0.29870130 1 0.5974026 0.5803340
+#> 71 51 24 2 0.32000000 1 0.6400000 0.6217143
+#> 72 66 15 2 0.18518519 1 0.3703704 0.3597884
+#> 73 50 10 2 0.16666667 1 0.3333333 0.3238095
+#> 74 37 8 2 0.17777778 1 0.3555556 0.3453968
+#> 75 63 14 2 0.18181818 1 0.3636364 0.3532468
+#> 76 57 19 2 0.25000000 1 0.5000000 0.4857143
+#> 77 53 17 2 0.24285714 1 0.4857143 0.4718367
+#> 78 59 9 2 0.13235294 1 0.2647059 0.2571429
+#> 79 39 12 2 0.23529412 1 0.4705882 0.4571429
+#> 80 59 18 2 0.23376623 1 0.4675325 0.4541744
+#> 81 64 14 2 0.17948718 1 0.3589744 0.3487179
+#> 82 56 13 2 0.18840580 1 0.3768116 0.3660455
+#> 83 53 12 2 0.18461538 1 0.3692308 0.3586813
+#> 84 54 17 2 0.23943662 1 0.4788732 0.4651911
+#> 85 57 22 2 0.27848101 1 0.5569620 0.5410488
+#> 86 47 15 2 0.24193548 1 0.4838710 0.4700461
+#> 87 48 20 2 0.29411765 1 0.5882353 0.5714286
+#> 88 54 9 2 0.14285714 1 0.2857143 0.2775510
+#> 89 54 9 2 0.14285714 1 0.2857143 0.2775510
+#> 90 65 15 2 0.18750000 1 0.3750000 0.3642857
+#> 91 58 12 2 0.17142857 1 0.3428571 0.3330612
+#> 92 55 13 2 0.19117647 1 0.3823529 0.3714286
+#> 93 44 16 2 0.26666667 1 0.5333333 0.5180952
+#> 94 63 20 2 0.24096386 1 0.4819277 0.4681583
+#> 95 63 20 2 0.24096386 1 0.4819277 0.4681583
+#> 96 55 8 2 0.12698413 1 0.2539683 0.2467120
+#> 97 64 16 2 0.20000000 1 0.4000000 0.3885714
+#> 98 49 20 2 0.28985507 1 0.5797101 0.5631470
+#> 99 67 15 2 0.18292683 1 0.3658537 0.3554007
+#> 100 55 25 2 0.31250000 1 0.6250000 0.6071429
+#> 101 68 22 2 0.24444444 1 0.4888889 0.4749206
+#> 102 57 11 2 0.16176471 1 0.3235294 0.3142857
+#> 103 56 16 2 0.22222222 1 0.4444444 0.4317460
+#> 104 72 15 2 0.17241379 1 0.3448276 0.3349754
+#> 105 66 18 2 0.21428571 1 0.4285714 0.4163265
+#> 106 67 14 2 0.17283951 1 0.3456790 0.3358025
+#> 107 58 7 2 0.10769231 1 0.2153846 0.2092308
+#> 108 53 8 2 0.13114754 1 0.2622951 0.2548009
+#> 109 56 18 2 0.24324324 1 0.4864865 0.4725869
+#> 110 50 21 2 0.29577465 1 0.5915493 0.5746479
+#> 111 59 10 2 0.14492754 1 0.2898551 0.2815735
+#> 112 65 17 2 0.20731707 1 0.4146341 0.4027875
+#> 113 63 13 2 0.17105263 1 0.3421053 0.3323308
+#> 114 55 13 2 0.19117647 1 0.3823529 0.3714286
+#> 115 61 13 2 0.17567568 1 0.3513514 0.3413127
+#> 116 62 20 2 0.24390244 1 0.4878049 0.4738676
+#> 117 65 20 2 0.23529412 1 0.4705882 0.4571429
+#> 118 51 14 2 0.21538462 1 0.4307692 0.4184615
+#> 119 69 20 2 0.22471910 1 0.4494382 0.4365971
+#> 120 47 13 2 0.21666667 1 0.4333333 0.4209524
+#> 121 58 16 2 0.21621622 1 0.4324324 0.4200772
+#> 122 55 19 2 0.25675676 1 0.5135135 0.4988417
+#> 123 60 13 2 0.17808219 1 0.3561644 0.3459883
+#> 124 62 23 2 0.27058824 1 0.5411765 0.5257143
+#> 125 61 24 2 0.28235294 1 0.5647059 0.5485714
+#> 126 63 12 2 0.16000000 1 0.3200000 0.3108571
+#> 127 44 18 2 0.29032258 1 0.5806452 0.5640553
+#> 128 54 16 2 0.22857143 1 0.4571429 0.4440816
+#> 129 64 21 2 0.24705882 1 0.4941176 0.4800000
+#> 130 43 14 2 0.24561404 1 0.4912281 0.4771930
+#> 131 68 18 2 0.20930233 1 0.4186047 0.4066445
+#> 132 56 21 2 0.27272727 1 0.5454545 0.5298701
+#> 133 63 16 2 0.20253165 1 0.4050633 0.3934901
+#> 134 57 18 2 0.24000000 1 0.4800000 0.4662857
+#> 135 46 10 2 0.17857143 1 0.3571429 0.3469388
+#> 136 44 18 2 0.29032258 1 0.5806452 0.5640553
+#> 137 51 15 2 0.22727273 1 0.4545455 0.4415584
+#> 138 61 17 2 0.21794872 1 0.4358974 0.4234432
+#> 139 50 15 2 0.23076923 1 0.4615385 0.4483516
+#> 140 35 21 2 0.37500000 1 0.7500000 0.7285714
+#> 141 42 17 2 0.28813559 1 0.5762712 0.5598063
+#> 142 40 18 2 0.31034483 1 0.6206897 0.6029557
+#> 143 39 21 2 0.35000000 1 0.7000000 0.6800000
+#> 144 47 13 2 0.21666667 1 0.4333333 0.4209524
+#> 145 46 12 2 0.20689655 1 0.4137931 0.4019704
+#> 146 42 13 2 0.23636364 1 0.4727273 0.4592208
+#> 147 54 14 2 0.20588235 1 0.4117647 0.4000000
+#> 148 58 22 2 0.27500000 1 0.5500000 0.5342857
+#> 149 64 14 2 0.17948718 1 0.3589744 0.3487179
+#> 150 60 17 2 0.22077922 1 0.4415584 0.4289425
+#> 151 41 11 2 0.21153846 1 0.4230769 0.4109890
+#> 152 60 16 2 0.21052632 1 0.4210526 0.4090226
+#> 153 70 22 2 0.23913043 1 0.4782609 0.4645963
+#> 154 54 17 2 0.23943662 1 0.4788732 0.4651911
+#> 155 58 19 2 0.24675325 1 0.4935065 0.4794063
+#> 156 58 12 2 0.17142857 1 0.3428571 0.3330612
+#> 157 50 15 2 0.23076923 1 0.4615385 0.4483516
+#> 158 55 15 2 0.21428571 1 0.4285714 0.4163265
+#> 159 54 14 2 0.20588235 1 0.4117647 0.4000000
+#> 160 72 22 2 0.23404255 1 0.4680851 0.4547112
+#> 161 56 15 2 0.21126761 1 0.4225352 0.4104628
+#> 162 56 22 2 0.28205128 1 0.5641026 0.5479853
+#> 163 70 23 2 0.24731183 1 0.4946237 0.4804916
+#> 164 55 24 2 0.30379747 1 0.6075949 0.5902351
+#> 165 62 12 2 0.16216216 1 0.3243243 0.3150579
+#> 166 54 15 2 0.21739130 1 0.4347826 0.4223602
+#> 167 70 14 2 0.16666667 1 0.3333333 0.3238095
+#> 168 47 21 2 0.30882353 1 0.6176471 0.6000000
+#> 169 46 14 2 0.23333333 1 0.4666667 0.4533333
+#> 170 75 14 2 0.15730337 1 0.3146067 0.3056180
+#> 171 61 22 2 0.26506024 1 0.5301205 0.5149742
+#> 172 52 17 2 0.24637681 1 0.4927536 0.4786749
+#> 173 51 13 2 0.20312500 1 0.4062500 0.3946429
+#> 174 52 12 2 0.18750000 1 0.3750000 0.3642857
+#> 175 70 11 2 0.13580247 1 0.2716049 0.2638448
+#> 176 59 16 2 0.21333333 1 0.4266667 0.4144762
+#> 177 62 12 2 0.16216216 1 0.3243243 0.3150579
+#> 178 51 18 2 0.26086957 1 0.5217391 0.5068323
+#> 179 67 16 2 0.19277108 1 0.3855422 0.3745267
+#> 180 63 21 2 0.25000000 1 0.5000000 0.4857143
+#> 181 77 13 2 0.14444444 1 0.2888889 0.2806349
+#> 182 55 18 2 0.24657534 1 0.4931507 0.4790607
+#> 183 59 17 2 0.22368421 1 0.4473684 0.4345865
+#> 184 60 16 2 0.21052632 1 0.4210526 0.4090226
+#> 185 57 14 2 0.19718310 1 0.3943662 0.3830986
+#> 186 58 13 2 0.18309859 1 0.3661972 0.3557344
+#> 187 66 21 2 0.24137931 1 0.4827586 0.4689655
+#> 188 62 18 2 0.22500000 1 0.4500000 0.4371429
+#> 189 53 21 2 0.28378378 1 0.5675676 0.5513514
+#> 190 56 22 2 0.28205128 1 0.5641026 0.5479853
+#> 191 61 12 2 0.16438356 1 0.3287671 0.3193738
+#> 192 56 19 2 0.25333333 1 0.5066667 0.4921905
+#> 193 54 20 2 0.27027027 1 0.5405405 0.5250965
+#> 194 51 16 2 0.23880597 1 0.4776119 0.4639659
+#> 195 44 20 2 0.31250000 1 0.6250000 0.6071429
+#> 196 56 24 2 0.30000000 1 0.6000000 0.5828571
+#> 197 66 19 2 0.22352941 1 0.4470588 0.4342857
+#> 198 50 20 2 0.28571429 1 0.5714286 0.5551020
+#> 199 51 14 2 0.21538462 1 0.4307692 0.4184615
+#> 200 75 16 2 0.17582418 1 0.3516484 0.3416013
+#> 201 70 21 2 0.23076923 1 0.4615385 0.4483516
+#> 202 58 16 2 0.21621622 1 0.4324324 0.4200772
+#> 203 51 18 2 0.26086957 1 0.5217391 0.5068323
+#> 204 49 20 2 0.28985507 1 0.5797101 0.5631470
+#> 205 58 16 2 0.21621622 1 0.4324324 0.4200772
+#> 206 46 18 2 0.28125000 1 0.5625000 0.5464286
+#> 207 57 18 2 0.24000000 1 0.4800000 0.4662857
+#> 208 65 18 2 0.21686747 1 0.4337349 0.4213425
+#> 209 40 25 2 0.38461538 1 0.7692308 0.7472527
+#> 210 40 25 2 0.38461538 1 0.7692308 0.7472527
+#> 211 55 18 2 0.24657534 1 0.4931507 0.4790607
+#> 212 74 18 2 0.19565217 1 0.3913043 0.3801242
+#> 213 56 19 2 0.25333333 1 0.5066667 0.4921905
+#> 214 59 16 2 0.21333333 1 0.4266667 0.4144762
+#> 215 71 14 2 0.16470588 1 0.3294118 0.3200000
+#> 216 61 15 2 0.19736842 1 0.3947368 0.3834586
+#> 217 46 23 2 0.33333333 1 0.6666667 0.6476190
+#> 218 64 19 2 0.22891566 1 0.4578313 0.4447504
+#> 219 62 12 2 0.16216216 1 0.3243243 0.3150579
+#> 220 57 19 2 0.25000000 1 0.5000000 0.4857143
+#> 221 64 12 2 0.15789474 1 0.3157895 0.3067669
+#> 222 50 16 2 0.24242424 1 0.4848485 0.4709957
+#> 223 53 16 2 0.23188406 1 0.4637681 0.4505176
+#> 224 61 16 2 0.20779221 1 0.4155844 0.4037106
+#> 225 59 28 2 0.32183908 1 0.6436782 0.6252874
+#> 226 65 25 2 0.27777778 1 0.5555556 0.5396825
+#> 227 63 10 2 0.13698630 1 0.2739726 0.2661448
+#> 228 53 7 2 0.11666667 1 0.2333333 0.2266667
+#> 229 50 14 2 0.21875000 1 0.4375000 0.4250000
+#> 230 61 16 2 0.20779221 1 0.4155844 0.4037106
+#> 231 54 10 2 0.15625000 1 0.3125000 0.3035714
+#> 232 56 17 2 0.23287671 1 0.4657534 0.4524462
+#> 233 61 17 2 0.21794872 1 0.4358974 0.4234432
+#> 234 54 12 2 0.18181818 1 0.3636364 0.3532468
+#> 235 54 12 2 0.18181818 1 0.3636364 0.3532468
+#> 236 54 14 2 0.20588235 1 0.4117647 0.4000000
+#> 237 50 16 2 0.24242424 1 0.4848485 0.4709957
+#> 238 61 14 2 0.18666667 1 0.3733333 0.3626667
+#> 239 67 18 2 0.21176471 1 0.4235294 0.4114286
+#> 240 47 7 2 0.12962963 1 0.2592593 0.2518519
+#> 241 63 16 2 0.20253165 1 0.4050633 0.3934901
+#> 242 60 15 2 0.20000000 1 0.4000000 0.3885714
+#> 243 55 19 2 0.25675676 1 0.5135135 0.4988417
+#> 244 50 11 2 0.18032787 1 0.3606557 0.3503513
+#> 245 52 15 2 0.22388060 1 0.4477612 0.4349680
+#> 246 56 28 2 0.33333333 1 0.6666667 0.6476190
+#> 247 55 9 2 0.14062500 1 0.2812500 0.2732143
+#> 248 52 12 2 0.18750000 1 0.3750000 0.3642857
+#> 249 42 10 2 0.19230769 1 0.3846154 0.3736264
+#> 250 78 26 2 0.25000000 1 0.5000000 0.4857143
+#> 251 79 26 2 0.24761905 1 0.4952381 0.4810884
+#> 252 55 15 2 0.21428571 1 0.4285714 0.4163265
+#> 253 54 15 2 0.21739130 1 0.4347826 0.4223602
+#> 254 42 11 2 0.20754717 1 0.4150943 0.4032345
+#> 255 47 12 2 0.20338983 1 0.4067797 0.3951574
+#> 256 53 10 2 0.15873016 1 0.3174603 0.3083900
+#> 257 47 14 2 0.22950820 1 0.4590164 0.4459016
+#> 258 59 19 2 0.24358974 1 0.4871795 0.4732601
+#> 259 49 12 2 0.19672131 1 0.3934426 0.3822014
+#> 260 78 12 2 0.13333333 1 0.2666667 0.2590476
+#> 261 56 14 2 0.20000000 1 0.4000000 0.3885714
+#> 262 60 22 2 0.26829268 1 0.5365854 0.5212544
+#> 263 48 8 2 0.14285714 1 0.2857143 0.2775510
+#> 264 68 22 2 0.24444444 1 0.4888889 0.4749206
+#> 265 43 25 2 0.36764706 1 0.7352941 0.7142857
+#> 266 51 18 2 0.26086957 1 0.5217391 0.5068323
+#> 267 67 19 2 0.22093023 1 0.4418605 0.4292359
+#> 268 66 13 2 0.16455696 1 0.3291139 0.3197107
+#> 269 57 14 2 0.19718310 1 0.3943662 0.3830986
+#> 270 57 16 2 0.21917808 1 0.4383562 0.4258317
+#> 271 54 20 2 0.27027027 1 0.5405405 0.5250965
+#> 272 70 14 2 0.16666667 1 0.3333333 0.3238095
+#> 273 54 10 2 0.15625000 1 0.3125000 0.3035714
+#> 274 61 23 2 0.27380952 1 0.5476190 0.5319728
+#> 275 56 21 2 0.27272727 1 0.5454545 0.5298701
+#> 276 46 12 2 0.20689655 1 0.4137931 0.4019704
+#> 277 65 17 2 0.20731707 1 0.4146341 0.4027875
+#> 278 55 18 2 0.24657534 1 0.4931507 0.4790607
+#> 279 63 9 2 0.12500000 1 0.2500000 0.2428571
+#> 280 40 17 2 0.29824561 1 0.5964912 0.5794486
+#> 281 38 14 2 0.26923077 1 0.5384615 0.5230769
+#> 282 63 25 2 0.28409091 1 0.5681818 0.5519481
+#> 283 50 17 2 0.25373134 1 0.5074627 0.4929638
+#> 284 42 10 2 0.19230769 1 0.3846154 0.3736264
+#> 285 63 14 2 0.18181818 1 0.3636364 0.3532468
+#> 286 64 24 2 0.27272727 1 0.5454545 0.5298701
+#> 287 61 15 2 0.19736842 1 0.3947368 0.3834586
+#> 288 60 23 2 0.27710843 1 0.5542169 0.5383821
+#> 289 57 14 2 0.19718310 1 0.3943662 0.3830986
+#> 290 30 12 2 0.28571429 1 0.5714286 0.5551020
+#> 291 44 19 2 0.30158730 1 0.6031746 0.5859410
+#> 292 46 16 2 0.25806452 1 0.5161290 0.5013825
+#> 293 30 16 2 0.34782609 1 0.6956522 0.6757764
+#> 294 37 13 2 0.26000000 1 0.5200000 0.5051429
+#> 295 36 14 2 0.28000000 1 0.5600000 0.5440000
+#> 296 40 14 2 0.25925926 1 0.5185185 0.5037037
+#> 297 56 15 2 0.21126761 1 0.4225352 0.4104628
+#> 298 32 16 2 0.33333333 1 0.6666667 0.6476190
+#> 299 35 15 2 0.30000000 1 0.6000000 0.5828571
+#> 300 64 14 2 0.17948718 1 0.3589744 0.3487179
+#> 301 48 16 2 0.25000000 1 0.5000000 0.4857143
+#> 302 57 15 2 0.20833333 1 0.4166667 0.4047619
+#> 303 58 19 2 0.24675325 1 0.4935065 0.4794063
+#> 304 58 22 2 0.27500000 1 0.5500000 0.5342857
+#> 305 47 21 2 0.30882353 1 0.6176471 0.6000000
+#> 306 72 10 2 0.12195122 1 0.2439024 0.2369338
+#> 307 72 20 2 0.21739130 1 0.4347826 0.4223602
+#> 308 44 17 2 0.27868852 1 0.5573770 0.5414520
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+#> 632 88 15 2 0.14563107 1 0.2912621 0.2829404
+#> 633 84 18 2 0.17647059 1 0.3529412 0.3428571
+#> 634 79 14 2 0.15053763 1 0.3010753 0.2924731
+#> 635 69 16 2 0.18823529 1 0.3764706 0.3657143
+#> 636 80 12 2 0.13043478 1 0.2608696 0.2534161
+#> 637 62 14 2 0.18421053 1 0.3684211 0.3578947
+#> 638 81 14 2 0.14736842 1 0.2947368 0.2863158
+#> 639 64 18 2 0.21951220 1 0.4390244 0.4264808
+#> 640 92 14 2 0.13207547 1 0.2641509 0.2566038
+#> 641 78 13 2 0.14285714 1 0.2857143 0.2775510
+#> 642 82 21 2 0.20388350 1 0.4077670 0.3961165
+#> 643 65 15 2 0.18750000 1 0.3750000 0.3642857
+#> 644 64 11 2 0.14666667 1 0.2933333 0.2849524
+#> 645 59 10 2 0.14492754 1 0.2898551 0.2815735
+#> 646 68 9 2 0.11688312 1 0.2337662 0.2270872
+#> 647 72 17 2 0.19101124 1 0.3820225 0.3711075
+#> 648 75 15 2 0.16666667 1 0.3333333 0.3238095
+#> 649 89 12 2 0.11881188 1 0.2376238 0.2308345
+#> 650 85 15 2 0.15000000 1 0.3000000 0.2914286
+#> 651 70 15 2 0.17647059 1 0.3529412 0.3428571
+#> 652 69 16 2 0.18823529 1 0.3764706 0.3657143
+#> 653 63 13 2 0.17105263 1 0.3421053 0.3323308
+#> 654 82 10 2 0.10869565 1 0.2173913 0.2111801
+#> 655 62 11 2 0.15068493 1 0.3013699 0.2927593
+#> 656 69 10 2 0.12658228 1 0.2531646 0.2459313
+#> 657 73 20 2 0.21505376 1 0.4301075 0.4178187
+#> 658 64 16 2 0.20000000 1 0.4000000 0.3885714
+#> 659 72 20 2 0.21739130 1 0.4347826 0.4223602
+#> 660 79 20 2 0.20202020 1 0.4040404 0.3924964
+#> 661 65 21 2 0.24418605 1 0.4883721 0.4744186
+#> 662 75 14 2 0.15730337 1 0.3146067 0.3056180
+#> 663 51 15 2 0.22727273 1 0.4545455 0.4415584
+#> 664 57 20 2 0.25974026 1 0.5194805 0.5046382
+#> 665 91 16 2 0.14953271 1 0.2990654 0.2905207
+#> 666 59 18 2 0.23376623 1 0.4675325 0.4541744
+#> 667 81 18 2 0.18181818 1 0.3636364 0.3532468
+#> 668 77 17 2 0.18085106 1 0.3617021 0.3513678
+#> 669 83 15 2 0.15306122 1 0.3061224 0.2973761
+#> 670 84 27 2 0.24324324 1 0.4864865 0.4725869
+#> 671 90 18 2 0.16666667 1 0.3333333 0.3238095
+#> 672 78 15 2 0.16129032 1 0.3225806 0.3133641
+#> 673 59 20 2 0.25316456 1 0.5063291 0.4918626
+#> 674 72 14 2 0.16279070 1 0.3255814 0.3162791
+#> 675 63 19 2 0.23170732 1 0.4634146 0.4501742
+#> 676 74 16 2 0.17777778 1 0.3555556 0.3453968
+#> 677 81 15 2 0.15625000 1 0.3125000 0.3035714
+#> 678 65 21 2 0.24418605 1 0.4883721 0.4744186
+#> 679 71 11 2 0.13414634 1 0.2682927 0.2606272
+#> 680 81 14 2 0.14736842 1 0.2947368 0.2863158
+#> 681 65 10 2 0.13333333 1 0.2666667 0.2590476
+#> 682 79 20 2 0.20202020 1 0.4040404 0.3924964
+#> 683 68 38 2 0.35849057 1 0.7169811 0.6964960
+#> 684 65 20 2 0.23529412 1 0.4705882 0.4571429
+#> 685 77 13 2 0.14444444 1 0.2888889 0.2806349
+#> 686 71 19 2 0.21111111 1 0.4222222 0.4101587
+#> 687 90 21 2 0.18918919 1 0.3783784 0.3675676
+#> 688 70 18 2 0.20454545 1 0.4090909 0.3974026
+#> 689 77 27 2 0.25961538 1 0.5192308 0.5043956
+#> 690 74 23 2 0.23711340 1 0.4742268 0.4606775
+#> 691 66 19 2 0.22352941 1 0.4470588 0.4342857
+#> 692 59 13 2 0.18055556 1 0.3611111 0.3507937
+#> 693 67 13 2 0.16250000 1 0.3250000 0.3157143
+#> 694 83 14 2 0.14432990 1 0.2886598 0.2804124
+#> 695 60 15 2 0.20000000 1 0.4000000 0.3885714
+#> 696 63 19 2 0.23170732 1 0.4634146 0.4501742
+#> 697 90 12 2 0.11764706 1 0.2352941 0.2285714
+#> 698 59 41 2 0.41000000 1 0.8200000 0.7965714
+#> 699 82 18 2 0.18000000 1 0.3600000 0.3497143
+#> 700 79 15 2 0.15957447 1 0.3191489 0.3100304
+#> 701 75 20 2 0.21052632 1 0.4210526 0.4090226
+#> 702 82 19 2 0.18811881 1 0.3762376 0.3654880
+#> 703 67 10 2 0.12987013 1 0.2597403 0.2523191
+#> 704 86 19 2 0.18095238 1 0.3619048 0.3515646
+#> 705 96 17 2 0.15044248 1 0.3008850 0.2922882
+#> 706 67 16 2 0.19277108 1 0.3855422 0.3745267
+#> 707 67 15 2 0.18292683 1 0.3658537 0.3554007
+#> 708 73 11 2 0.13095238 1 0.2619048 0.2544218
+#> 709 67 16 2 0.19277108 1 0.3855422 0.3745267
+#> 710 63 17 2 0.21250000 1 0.4250000 0.4128571
+#> 711 56 30 2 0.34883721 1 0.6976744 0.6777409
+#> 712 68 10 2 0.12820513 1 0.2564103 0.2490842
+#> 713 71 20 2 0.21978022 1 0.4395604 0.4270016
+#> 714 74 20 2 0.21276596 1 0.4255319 0.4133739
+#> 715 72 20 2 0.21739130 1 0.4347826 0.4223602
+#> 716 56 15 2 0.21126761 1 0.4225352 0.4104628
+#> 717 69 17 2 0.19767442 1 0.3953488 0.3840532
+#> 718 72 12 2 0.14285714 1 0.2857143 0.2775510
+#> 719 85 14 2 0.14141414 1 0.2828283 0.2747475
+#> 720 79 12 2 0.13186813 1 0.2637363 0.2562009
+#> 721 65 16 2 0.19753086 1 0.3950617 0.3837743
+#> 722 65 13 2 0.16666667 1 0.3333333 0.3238095
+#> 723 71 13 2 0.15476190 1 0.3095238 0.3006803
+#> 724 80 10 2 0.11111111 1 0.2222222 0.2158730
+#> 725 90 16 2 0.15094340 1 0.3018868 0.2932615
+#> 726 67 15 2 0.18292683 1 0.3658537 0.3554007
+#> 727 87 16 2 0.15533981 1 0.3106796 0.3018031
+#> 728 60 10 2 0.14285714 1 0.2857143 0.2775510
+#> 729 63 16 2 0.20253165 1 0.4050633 0.3934901
+#> 730 68 12 2 0.15000000 1 0.3000000 0.2914286
+#> 731 72 19 2 0.20879121 1 0.4175824 0.4056515
+#> 732 88 20 2 0.18518519 1 0.3703704 0.3597884
+#> 733 55 11 2 0.16666667 1 0.3333333 0.3238095
+#> 734 74 14 2 0.15909091 1 0.3181818 0.3090909
+#> 735 70 19 2 0.21348315 1 0.4269663 0.4147673
+#> 736 76 20 2 0.20833333 1 0.4166667 0.4047619
+#> 737 73 16 2 0.17977528 1 0.3595506 0.3492777
+#> 738 72 16 2 0.18181818 1 0.3636364 0.3532468
+#> 739 63 19 2 0.23170732 1 0.4634146 0.4501742
+#> 740 59 17 2 0.22368421 1 0.4473684 0.4345865
+#> 741 80 18 2 0.18367347 1 0.3673469 0.3568513
+#> 742 91 22 2 0.19469027 1 0.3893805 0.3782554
+#> 743 69 14 2 0.16867470 1 0.3373494 0.3277108
+#> 744 54 34 2 0.38636364 1 0.7727273 0.7506494
+#> 745 79 21 2 0.21000000 1 0.4200000 0.4080000
+#> 746 81 16 2 0.16494845 1 0.3298969 0.3204713
+#> 747 129 20 2 0.13422819 1 0.2684564 0.2607862
+#> 748 71 13 2 0.15476190 1 0.3095238 0.3006803
+#> 749 53 26 2 0.32911392 1 0.6582278 0.6394213
+#> 750 71 18 2 0.20224719 1 0.4044944 0.3929374
+#> 751 87 23 2 0.20909091 1 0.4181818 0.4062338
+#> 752 78 12 2 0.13333333 1 0.2666667 0.2590476
+#> 753 82 15 2 0.15463918 1 0.3092784 0.3004418
+#> 754 80 17 2 0.17525773 1 0.3505155 0.3405007
+#> 755 72 13 2 0.15294118 1 0.3058824 0.2971429
+#> 756 64 24 2 0.27272727 1 0.5454545 0.5298701
+#> 757 52 37 2 0.41573034 1 0.8314607 0.8077047
+#> 758 76 16 2 0.17391304 1 0.3478261 0.3378882
+#> 759 66 10 2 0.13157895 1 0.2631579 0.2556391
+#> 760 74 20 2 0.21276596 1 0.4255319 0.4133739
+#> 761 71 22 2 0.23655914 1 0.4731183 0.4596006
+#> 762 79 12 2 0.13186813 1 0.2637363 0.2562009
+#> 763 66 19 2 0.22352941 1 0.4470588 0.4342857
+#> 764 62 12 2 0.16216216 1 0.3243243 0.3150579
+#> 765 72 21 2 0.22580645 1 0.4516129 0.4387097
+#> 766 57 23 2 0.28750000 1 0.5750000 0.5585714
+#> 767 71 16 2 0.18390805 1 0.3678161 0.3573071
+#> 768 62 11 2 0.15068493 1 0.3013699 0.2927593
+#> 769 68 17 2 0.20000000 1 0.4000000 0.3885714
+#> CCF_sample
+#> 1 1.5703442
+#> 2 1.1182754
+#> 3 1.2317236
+#> 4 0.7613790
+#> 5 0.8946203
+#> 6 0.8226394
+#> 7 0.8182503
+#> 8 1.0896017
+#> 9 1.0880517
+#> 10 0.7198094
+#> 11 0.7741907
+#> 12 0.7062792
+#> 13 0.9191305
+#> 14 0.8462625
+#> 15 1.2546504
+#> 16 1.0005622
+#> 17 1.3916316
+#> 18 0.8089652
+#> 19 0.8387065
+#> 20 1.2986424
+#> 21 0.7560172
+#> 22 1.0322542
+#> 23 1.0843883
+#> 24 0.6127536
+#> 25 1.0322542
+#> 26 1.0005622
+#> 27 1.0524945
+#> 28 0.4523361
+#> 29 1.0191877
+#> 30 1.1455504
+#> 31 1.0372409
+#> 32 0.9585218
+#> 33 1.1825441
+#> 34 0.8602118
+#> 35 1.2425282
+#> 36 0.8828490
+#> 37 1.0735444
+#> 38 0.7281793
+#> 39 1.0492460
+#> 40 0.9036569
+#> 41 1.0843883
+#> 42 0.9041375
+#> 43 1.0561490
+#> 44 1.0456601
+#> 45 0.9059446
+#> 46 1.3724289
+#> 47 1.0822020
+#> 48 1.2264956
+#> 49 1.1037523
+#> 50 1.3230300
+#> 51 0.9417056
+#> 52 1.0191877
+#> 53 1.2877111
+#> 54 0.7544991
+#> 55 0.4970113
+#> 56 1.0322542
+#> 57 1.0594188
+#> 58 0.8946203
+#> 59 1.1856414
+#> 60 1.3490306
+#> 61 1.2017288
+#> 62 0.9379084
+#> 63 1.2255073
+#> 64 0.9379084
+#> 65 1.1771320
+#> 66 0.7801921
+#> 67 1.2684915
+#> 68 1.2247778
+#> 69 0.6127536
+#> 70 1.3361212
+#> 71 1.4313925
+#> 72 0.8283521
+#> 73 0.7455169
+#> 74 0.7952181
+#> 75 0.8132912
+#> 76 1.1182754
+#> 77 1.0863247
+#> 78 0.5920281
+#> 79 1.0524945
+#> 80 1.0456601
+#> 81 0.8028644
+#> 82 0.8427583
+#> 83 0.8258034
+#> 84 1.0710243
+#> 85 1.2456739
+#> 86 1.0822020
+#> 87 1.3156181
+#> 88 0.6390145
+#> 89 0.6390145
+#> 90 0.8387065
+#> 91 0.7668174
+#> 92 0.8551518
+#> 93 1.1928271
+#> 94 1.0778558
+#> 95 1.0778558
+#> 96 0.5680129
+#> 97 0.8946203
+#> 98 1.2965512
+#> 99 0.8182503
+#> 100 1.3978442
+#> 101 1.0934248
+#> 102 0.7235900
+#> 103 0.9940226
+#> 104 0.7712244
+#> 105 0.9585218
+#> 106 0.7731287
+#> 107 0.4817186
+#> 108 0.5866363
+#> 109 1.0880517
+#> 110 1.3230300
+#> 111 0.6482756
+#> 112 0.9273503
+#> 113 0.7651358
+#> 114 0.8551518
+#> 115 0.7858151
+#> 116 1.0910004
+#> 117 1.0524945
+#> 118 0.9634373
+#> 119 1.0051914
+#> 120 0.9691720
+#> 121 0.9671571
+#> 122 1.1484990
+#> 123 0.7965797
+#> 124 1.2103687
+#> 125 1.2629934
+#> 126 0.7156962
+#> 127 1.2986424
+#> 128 1.0224232
+#> 129 1.1051192
+#> 130 1.0986565
+#> 131 0.9362306
+#> 132 1.2199368
+#> 133 0.9059446
+#> 134 1.0735444
+#> 135 0.7987681
+#> 136 1.2986424
+#> 137 1.0166140
+#> 138 0.9749068
+#> 139 1.0322542
+#> 140 1.6774131
+#> 141 1.2888598
+#> 142 1.3882039
+#> 143 1.5655855
+#> 144 0.9691720
+#> 145 0.9254693
+#> 146 1.0572786
+#> 147 0.9209327
+#> 148 1.2301029
+#> 149 0.8028644
+#> 150 0.9875679
+#> 151 0.9462330
+#> 152 0.9417056
+#> 153 1.0696547
+#> 154 1.0710243
+#> 155 1.1037523
+#> 156 0.7668174
+#> 157 1.0322542
+#> 158 0.9585218
+#> 159 0.9209327
+#> 160 1.0468961
+#> 161 0.9450215
+#> 162 1.2616440
+#> 163 1.1062509
+#> 164 1.3589169
+#> 165 0.7253678
+#> 166 0.9724134
+#> 167 0.7455169
+#> 168 1.3813990
+#> 169 1.0437237
+#> 170 0.7036340
+#> 171 1.1856414
+#> 172 1.1020685
+#> 173 0.9085988
+#> 174 0.8387065
+#> 175 0.6074582
+#> 176 0.9542617
+#> 177 0.7253678
+#> 178 1.1668961
+#> 179 0.8622846
+#> 180 1.1182754
+#> 181 0.6461147
+#> 182 1.1029565
+#> 183 1.0005622
+#> 184 0.9417056
+#> 185 0.8820200
+#> 186 0.8190186
+#> 187 1.0797142
+#> 188 1.0064479
+#> 189 1.2693937
+#> 190 1.2616440
+#> 191 0.7353044
+#> 192 1.1331857
+#> 193 1.2089464
+#> 194 1.0682034
+#> 195 1.3978442
+#> 196 1.3419305
+#> 197 0.9998698
+#> 198 1.2780290
+#> 199 0.9634373
+#> 200 0.7864794
+#> 201 1.0322542
+#> 202 0.9671571
+#> 203 1.1668961
+#> 204 1.2965512
+#> 205 0.9671571
+#> 206 1.2580598
+#> 207 1.0735444
+#> 208 0.9700702
+#> 209 1.7204237
+#> 210 1.7204237
+#> 211 1.1029565
+#> 212 0.8751720
+#> 213 1.1331857
+#> 214 0.9542617
+#> 215 0.7367461
+#> 216 0.8828490
+#> 217 1.4910339
+#> 218 1.0239630
+#> 219 0.7253678
+#> 220 1.1182754
+#> 221 0.7062792
+#> 222 1.0843883
+#> 223 1.0372409
+#> 224 0.9294756
+#> 225 1.4396189
+#> 226 1.2425282
+#> 227 0.6127536
+#> 228 0.5218618
+#> 229 0.9784910
+#> 230 0.9294756
+#> 231 0.6989221
+#> 232 1.0416812
+#> 233 0.9749068
+#> 234 0.8132912
+#> 235 0.8132912
+#> 236 0.9209327
+#> 237 1.0843883
+#> 238 0.8349790
+#> 239 0.9472450
+#> 240 0.5798465
+#> 241 0.9059446
+#> 242 0.8946203
+#> 243 1.1484990
+#> 244 0.8066249
+#> 245 1.0014406
+#> 246 1.4910339
+#> 247 0.6290299
+#> 248 0.8387065
+#> 249 0.8602118
+#> 250 1.1182754
+#> 251 1.1076251
+#> 252 0.9585218
+#> 253 0.9724134
+#> 254 0.9283796
+#> 255 0.9097834
+#> 256 0.7100161
+#> 257 1.0266135
+#> 258 1.0896017
+#> 259 0.8799544
+#> 260 0.5964135
+#> 261 0.8946203
+#> 262 1.2001004
+#> 263 0.6390145
+#> 264 1.0934248
+#> 265 1.6445226
+#> 266 1.1668961
+#> 267 0.9882434
+#> 268 0.7360800
+#> 269 0.8820200
+#> 270 0.9804058
+#> 271 1.2089464
+#> 272 0.7455169
+#> 273 0.6989221
+#> 274 1.2247778
+#> 275 1.2199368
+#> 276 0.9254693
+#> 277 0.9273503
+#> 278 1.1029565
+#> 279 0.5591377
+#> 280 1.3340829
+#> 281 1.2042966
+#> 282 1.2707675
+#> 283 1.1349661
+#> 284 0.8602118
+#> 285 0.8132912
+#> 286 1.2199368
+#> 287 0.8828490
+#> 288 1.2395342
+#> 289 0.8820200
+#> 290 1.2780290
+#> 291 1.3490306
+#> 292 1.1543488
+#> 293 1.5558614
+#> 294 1.1630064
+#> 295 1.2524684
+#> 296 1.1596930
+#> 297 0.9450215
+#> 298 1.4910339
+#> 299 1.3419305
+#> 300 0.8028644
+#> 301 1.1182754
+#> 302 0.9318962
+#> 303 1.1037523
+#> 304 1.2301029
+#> 305 1.3813990
+#> 306 0.5455002
+#> 307 0.9724134
+#> 308 1.2466021
+#> 309 1.0880517
+#> 310 1.1455504
+#> 311 1.1577439
+#> 312 1.1840563
+#> 313 0.9700702
+#> 314 1.3189915
+#> 315 1.2867826
+#> 316 1.1182754
+#> 317 0.8544127
+#> 318 1.5872296
+#> 319 1.3253634
+#> 320 0.5964135
+#> 321 1.2141276
+#> 322 0.7100161
+#> 323 1.2149165
+#> 324 0.9318962
+#> 325 1.3121098
+#> 326 0.8520193
+#> 327 0.8946203
+#> 328 0.8641219
+#> 329 0.8551518
+#> 330 0.6777427
+#> 331 0.8810655
+#> 332 0.4771308
+#> 333 1.4289074
+#> 334 1.0100552
+#> 335 1.2395342
+#> 336 1.1386077
+#> 337 0.8300601
+#> 338 0.7827928
+#> 339 0.6099684
+#> 340 0.6930157
+#> 341 0.8258034
+#> 342 0.8828490
+#> 343 1.0064479
+#> 344 1.0005622
+#> 345 0.7893709
+#> 346 0.7965797
+#> 347 1.5376287
+#> 348 1.1182754
+#> 349 1.1771320
+#> 350 1.3902883
+#> 351 0.8258034
+#> 352 0.9149526
+#> 353 1.3589169
+#> 354 0.6390145
+#> 355 0.9450215
+#> 356 0.9387991
+#> 357 0.6676271
+#> 358 1.2673788
+#> 359 0.9724134
+#> 360 0.7893709
+#> 361 1.2466021
+#> 362 1.2141276
+#> 363 1.0896017
+#> 364 0.8946203
+#> 365 1.0468961
+#> 366 1.1360258
+#> 367 1.2017288
+#> 368 1.0166140
+#> 369 0.9346779
+#> 370 0.7029160
+#> 371 0.9191305
+#> 372 1.2456739
+#> 373 0.9387991
+#> 374 1.1311291
+#> 375 0.7353044
+#> 376 1.2001004
+#> 377 1.1881676
+#> 378 1.4043458
+#> 379 1.3537018
+#> 380 1.4183005
+#> 381 0.6546002
+#> 382 0.8602118
+#> 383 1.0650242
+#> 384 1.1568366
+#> 385 1.2339591
+#> 386 0.4066456
+#> 387 0.9387991
+#> 388 0.8011525
+#> 389 0.9472450
+#> 390 1.2017288
+#> 391 0.7965797
+#> 392 1.1469491
+#> 393 0.7235900
+#> 394 1.5163056
+#> 395 1.0191877
+#> 396 0.7455169
+#> 397 1.1771320
+#> 398 1.0682034
+#> 399 0.6649205
+#> 400 0.8387065
+#> 401 0.9625662
+#> 402 0.9784910
+#> 403 1.0166140
+#> 404 0.7952181
+#> 405 1.1182754
+#> 406 0.7753376
+#> 407 0.7712244
+#> 408 0.9222890
+#> 409 0.8028644
+#> 410 0.8011525
+#> 411 0.9585218
+#> 412 0.9339443
+#> 413 1.1642319
+#> 414 1.5150828
+#> 415 0.8182503
+#> 416 0.9191305
+#> 417 0.7544991
+#> 418 0.8076433
+#> 419 1.0014406
+#> 420 0.8679152
+#> 421 1.2466021
+#> 422 1.1856414
+#> 423 1.2867826
+#> 424 0.8226394
+#> 425 1.0524945
+#> 426 0.8842178
+#> 427 0.6228369
+#> 428 1.2400678
+#> 429 1.2466021
+#> 430 1.2780290
+#> 431 0.9417056
+#> 432 0.9634373
+#> 433 0.9691720
+#> 434 0.7137928
+#> 435 0.9940226
+#> 436 0.7281793
+#> 437 0.5341017
+#> 438 0.7360800
+#> 439 1.1295711
+#> 440 1.1182754
+#> 441 0.8076433
+#> 442 0.8835756
+#> 443 1.1521625
+#> 444 1.0005622
+#> 445 0.8835756
+#> 446 1.1596930
+#> 447 1.0650242
+#> 448 0.8427583
+#> 449 0.8946203
+#> 450 1.2600286
+#> 451 1.2130445
+#> 452 1.1331857
+#> 453 0.8835756
+#> 454 1.1804018
+#> 455 0.6833905
+#> 456 0.7936148
+#> 457 1.1618446
+#> 458 1.2780290
+#> 459 0.8239924
+#> 460 1.1010712
+#> 461 0.9505341
+#> 462 1.1037523
+#> 463 1.2255073
+#> 464 1.0572786
+#> 465 0.9855986
+#> 466 0.8828490
+#> 467 1.1010712
+#> 468 0.8339681
+#> 469 1.1596930
+#> 470 0.8946203
+#> 471 1.1521625
+#> 472 0.8565514
+#> 473 1.1182754
+#> 474 1.1182754
+#> 475 0.8622846
+#> 476 0.7595833
+#> 477 0.9804058
+#> 478 0.8419956
+#> 479 1.3279520
+#> 480 0.7343898
+#> 481 0.9867136
+#> 482 1.0880517
+#> 483 0.9175593
+#> 484 0.8011525
+#> 485 0.9191305
+#> 486 0.7551990
+#> 487 1.1840563
+#> 488 0.8946203
+#> 489 0.7235900
+#> 490 0.8387065
+#> 491 0.6390145
+#> 492 1.1618446
+#> 493 0.9472450
+#> 494 0.9191305
+#> 495 0.9075858
+#> 496 0.8946203
+#> 497 1.0005622
+#> 498 1.0758092
+#> 499 1.3156181
+#> 500 0.8427583
+#> 501 1.5716303
+#> 502 1.1340257
+#> 503 1.1668961
+#> 504 1.1741892
+#> 505 0.7551990
+#> 506 0.9417056
+#> 507 0.6193525
+#> 508 1.0986565
+#> 509 0.8740543
+#> 510 0.8190186
+#> 511 0.7927015
+#> 512 1.2001004
+#> 513 0.5920281
+#> 514 0.7455169
+#> 515 1.2395342
+#> 516 1.0276044
+#> 517 0.8820200
+#> 518 1.0910004
+#> 519 1.0561490
+#> 520 0.9585218
+#> 521 1.1648702
+#> 522 0.9671571
+#> 523 0.9940226
+#> 524 0.9175593
+#> 525 0.7987681
+#> 526 0.8200686
+#> 527 0.9417056
+#> 528 1.0322542
+#> 529 1.0456601
+#> 530 0.8182503
+#> 531 1.1771320
+#> 532 0.9784910
+#> 533 1.0650242
+#> 534 0.8132912
+#> 535 1.0266135
+#> 536 1.2425282
+#> 537 0.4005763
+#> 538 1.0372409
+#> 539 0.8462625
+#> 540 0.9585218
+#> 541 1.2659721
+#> 542 0.9882434
+#> 543 0.9867136
+#> 544 0.8132912
+#> 545 0.9940226
+#> 546 1.0623616
+#> 547 1.0863247
+#> 548 0.9387991
+#> 549 1.1668961
+#> 550 1.1324308
+#> 551 0.9940226
+#> 552 0.8349790
+#> 553 0.8387065
+#> 554 1.0224232
+#> 555 1.1051192
+#> 556 1.3003202
+#> 557 0.9462330
+#> 558 0.6833905
+#> 559 1.0843883
+#> 560 1.1311291
+#> 561 1.1182754
+#> 562 0.9318962
+#> 563 1.0594188
+#> 564 1.1771320
+#> 565 0.8483468
+#> 566 1.0456601
+#> 567 0.9804058
+#> 568 1.0843883
+#> 569 1.0922690
+#> 570 1.1559701
+#> 571 1.1698881
+#> 572 0.9085988
+#> 573 0.9379084
+#> 574 1.3480580
+#> 575 1.0524945
+#> 576 1.1349661
+#> 577 1.2359886
+#> 578 1.0100552
+#> 579 0.6676271
+#> 580 1.3667810
+#> 581 0.8132912
+#> 582 0.8239924
+#> 583 0.6930157
+#> 584 1.1732725
+#> 585 1.1502261
+#> 586 1.1182754
+#> 587 1.0166140
+#> 588 0.7810177
+#> 589 0.6626817
+#> 590 0.6733701
+#> 591 1.0201811
+#> 592 0.8356344
+#> 593 0.7668174
+#> 594 1.2780290
+#> 595 0.7779307
+#> 596 1.1182754
+#> 597 1.2017288
+#> 598 0.6523273
+#> 599 0.9209327
+#> 600 0.6390145
+#> 601 0.9294756
+#> 602 0.9940226
+#> 603 0.8740543
+#> 604 0.8520193
+#> 605 1.0210341
+#> 606 0.8946203
+#> 607 0.8632301
+#> 608 0.7367461
+#> 609 0.9462330
+#> 610 1.0843883
+#> 611 1.1928271
+#> 612 1.6179304
+#> 613 1.1771320
+#> 614 1.6103166
+#> 615 1.4687796
+#> 616 1.1360258
+#> 617 1.5655855
+#> 618 0.6390145
+#> 619 1.1442818
+#> 620 1.2888598
+#> 621 1.0999430
+#> 622 1.6981219
+#> 623 1.8775982
+#> 624 0.6057325
+#> 625 0.8751720
+#> 626 0.7839456
+#> 627 1.0250858
+#> 628 0.8728003
+#> 629 0.8041531
+#> 630 0.5857633
+#> 631 1.3103025
+#> 632 0.6514226
+#> 633 0.7893709
+#> 634 0.6733701
+#> 635 0.8419956
+#> 636 0.5834480
+#> 637 0.8239924
+#> 638 0.6591939
+#> 639 0.9819003
+#> 640 0.5907870
+#> 641 0.6390145
+#> 642 0.9119916
+#> 643 0.8387065
+#> 644 0.6560549
+#> 645 0.6482756
+#> 646 0.5228301
+#> 647 0.8544127
+#> 648 0.7455169
+#> 649 0.5314576
+#> 650 0.6709652
+#> 651 0.7893709
+#> 652 0.8419956
+#> 653 0.7651358
+#> 654 0.4862067
+#> 655 0.6740290
+#> 656 0.5662154
+#> 657 0.9619573
+#> 658 0.8946203
+#> 659 0.9724134
+#> 660 0.9036569
+#> 661 1.0922690
+#> 662 0.7036340
+#> 663 1.0166140
+#> 664 1.1618446
+#> 665 0.6688750
+#> 666 1.0456601
+#> 667 0.8132912
+#> 668 0.8089652
+#> 669 0.6846584
+#> 670 1.0880517
+#> 671 0.7455169
+#> 672 0.7214680
+#> 673 1.1324308
+#> 674 0.7281793
+#> 675 1.0364504
+#> 676 0.7952181
+#> 677 0.6989221
+#> 678 1.0922690
+#> 679 0.6000502
+#> 680 0.6591939
+#> 681 0.5964135
+#> 682 0.9036569
+#> 683 1.6035647
+#> 684 1.0524945
+#> 685 0.6461147
+#> 686 0.9443214
+#> 687 0.8462625
+#> 688 0.9149526
+#> 689 1.1612860
+#> 690 1.0606323
+#> 691 0.9998698
+#> 692 0.8076433
+#> 693 0.7268790
+#> 694 0.6456023
+#> 695 0.8946203
+#> 696 1.0364504
+#> 697 0.5262472
+#> 698 1.8339716
+#> 699 0.8051583
+#> 700 0.7137928
+#> 701 0.9417056
+#> 702 0.8414746
+#> 703 0.5809223
+#> 704 0.8094184
+#> 705 0.6729445
+#> 706 0.8622846
+#> 707 0.8182503
+#> 708 0.5857633
+#> 709 0.8622846
+#> 710 0.9505341
+#> 711 1.5603843
+#> 712 0.5734746
+#> 713 0.9830992
+#> 714 0.9517237
+#> 715 0.9724134
+#> 716 0.9450215
+#> 717 0.8842178
+#> 718 0.6390145
+#> 719 0.6325598
+#> 720 0.5898595
+#> 721 0.8835756
+#> 722 0.7455169
+#> 723 0.6922657
+#> 724 0.4970113
+#> 725 0.6751851
+#> 726 0.8182503
+#> 727 0.6948507
+#> 728 0.6390145
+#> 729 0.9059446
+#> 730 0.6709652
+#> 731 0.9339443
+#> 732 0.8283521
+#> 733 0.7455169
+#> 734 0.7116298
+#> 735 0.9549318
+#> 736 0.9318962
+#> 737 0.8041531
+#> 738 0.8132912
+#> 739 1.0364504
+#> 740 1.0005622
+#> 741 0.8215901
+#> 742 0.8708693
+#> 743 0.7544991
+#> 744 1.7282438
+#> 745 0.9393513
+#> 746 0.7378312
+#> 747 0.6004163
+#> 748 0.6922657
+#> 749 1.4721600
+#> 750 0.9046722
+#> 751 0.9352849
+#> 752 0.5964135
+#> 753 0.6917167
+#> 754 0.7839456
+#> 755 0.6841214
+#> 756 1.2199368
+#> 757 1.8596040
+#> 758 0.7779307
+#> 759 0.5885660
+#> 760 0.9517237
+#> 761 1.0581531
+#> 762 0.5898595
+#> 763 0.9998698
+#> 764 0.7253678
+#> 765 1.0100552
+#> 766 1.2860167
+#> 767 0.8226394
+#> 768 0.6740290
+#> 769 0.8946203
+#> [ reached 'max' / getOption("max.print") -- omitted 3843 rows ]
+#>
#estimate purity based sole on a smaple ID + added seg data.
estimate_purity(this_sample_id = "HTMCP-01-06-00422-01A-01D",
show_plots = TRUE, coding_only = TRUE)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+#> $VAF_plot
+#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
+
+#>
+#> $Purity_plot
+#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
+
+#>
+#> $sample_purity_estimation
+#> [1] 0.4483024
+#>
+#> $CN_final
+#> Hugo_Symbol Chrom_pos Chromosome Start_Position End_Position
+#> 1 BTG2 1:203274877 1 203274877 203274877
+#> 2 BTG2 1:203274883 1 203274883 203274883
+#> 3 DUSP2 2:96809892 2 96809892 96809892
+#> 4 USP38 4:144135996 4 144135996 144135996
+#> 5 DDX60 4:169195215 4 169195215 169195215
+#> 6 ZFR 5:32417803 5 32417803 32417803
+#> 7 HIST1H1E 6:26157109 6 26157109 26157109
+#> 8 HIST1H4H 6:26285627 6 26285627 26285627
+#> 9 PIM1 6:37138549 6 37138549 37138549
+#> 10 MYO6 6:76602374 6 76602374 76602374
+#> 11 ADGB 6:147090183 6 147090183 147090183
+#> 12 MEOX2 7:15652211 7 15652211 15652211
+#> 13 SAMD9L 7:92763210 7 92763210 92763210
+#> 14 MUC12 7:100635711 7 100635711 100635711
+#> 15 CYB561A3 11:61118471 11 61118471 61118471
+#> 16 B4GALNT3 12:661271 12 661271 661272
+#> 17 RERGL 12:18237497 12 18237497 18237497
+#> 18 SLCO1A2 12:21453503 12 21453503 21453503
+#> 19 HECTD4 12:112746674 12 112746674 112746674
+#> 20 KIAA0226L 13:46961263 13 46961263 46961263
+#> 21 ZFP36L1 14:69257090 14 69257090 69257090
+#> 22 ZFP36L1 14:69259603 14 69259603 69259603
+#> 23 IGHG2 14:106109960 14 106109960 106109960
+#> 24 IGHG2 14:106110428 14 106110428 106110428
+#> 25 IGHG2 14:106110883 14 106110883 106110883
+#> 26 IGHG1 14:106208502 14 106208502 106208502
+#> 27 IGHV1-8 14:106539389 14 106539389 106539389
+#> 28 SCNN1G 16:23200859 16 23200859 23200859
+#> 29 SNPH 20:1285578 20 1285578 1285578
+#> 30 LZTS3 20:3147779 20 3147779 3147779
+#> 31 TRPM1 15:31319180 15 31319180 31319180
+#> 32 C17orf77 17:72588641 17 72588641 72588641
+#> 33 RP11-1055B8.7 17:79430805 17 79430805 79430805
+#> 34 CLPP 19:6361633 19 6361633 6361633
+#> 35 ACTR5 20:37378710 20 37378710 37378710
+#> 36 RAX 18:56936659 18 56936659 56936659
+#> 37 BOC 3:112993366 3 112993366 112993366
+#> 38 USP13 3:179499554 3 179499554 179499554
+#> t_ref_count t_alt_count CN VAF Ploidy Purity CCF_mutation
+#> 1 78 26 2 0.2500000 1 0.5000000 0.8020833
+#> 2 79 26 2 0.2476190 1 0.4952381 0.7944444
+#> 3 67 15 2 0.1829268 1 0.3658537 0.5868902
+#> 4 63 15 2 0.1923077 1 0.3846154 0.6169872
+#> 5 60 19 2 0.2405063 1 0.4810127 0.7716245
+#> 6 54 21 2 0.2800000 1 0.5600000 0.8983333
+#> 7 63 15 2 0.1923077 1 0.3846154 0.6169872
+#> 8 64 12 2 0.1578947 1 0.3157895 0.5065789
+#> 9 60 17 2 0.2207792 1 0.4415584 0.7083333
+#> 10 67 15 2 0.1829268 1 0.3658537 0.5868902
+#> 11 59 18 2 0.2337662 1 0.4675325 0.7500000
+#> 12 51 19 2 0.2714286 1 0.5428571 0.8708333
+#> 13 41 16 2 0.2807018 1 0.5614035 0.9005848
+#> 14 71 19 2 0.2111111 1 0.4222222 0.6773148
+#> 15 46 18 2 0.2812500 1 0.5625000 0.9023438
+#> 16 59 17 2 0.2236842 1 0.4473684 0.7176535
+#> 17 54 15 2 0.2173913 1 0.4347826 0.6974638
+#> 18 55 16 2 0.2253521 1 0.4507042 0.7230047
+#> 19 67 11 2 0.1410256 1 0.2820513 0.4524573
+#> 20 53 20 2 0.2739726 1 0.5479452 0.8789954
+#> 21 60 16 2 0.2105263 1 0.4210526 0.6754386
+#> 22 71 17 2 0.1931818 1 0.3863636 0.6197917
+#> 23 53 24 2 0.3116883 1 0.6233766 1.0000000
+#> 24 62 21 2 0.2530120 1 0.5060241 0.8117470
+#> 25 63 17 2 0.2125000 1 0.4250000 0.6817708
+#> 26 61 15 2 0.1973684 1 0.3947368 0.6332237
+#> 27 60 13 2 0.1780822 1 0.3561644 0.5713470
+#> 28 68 18 2 0.2093023 1 0.4186047 0.6715116
+#> 29 56 16 2 0.2222222 1 0.4444444 0.7129630
+#> 30 65 24 2 0.2696629 1 0.5393258 0.8651685
+#> 31 53 11 2 0.1718750 1 0.3437500 0.5514323
+#> 32 72 19 2 0.2087912 1 0.4175824 0.6698718
+#> 33 68 21 2 0.2359551 1 0.4719101 0.7570225
+#> 34 80 29 2 0.2660550 1 0.5321101 0.8535933
+#> 35 44 19 1 0.3015873 1 0.3015873 0.4837963
+#> 36 104 31 4 0.2296296 2 0.4592593 0.7367284
+#> 37 70 28 3 0.2857143 2 0.4285714 0.6875000
+#> 38 71 16 3 0.1839080 1 0.5517241 0.8850575
+#> CCF_sample
+#> 1 1.1153186
+#> 2 1.1046965
+#> 3 0.8160867
+#> 4 0.8579373
+#> 5 1.0729647
+#> 6 1.2491568
+#> 7 0.8579373
+#> 8 0.7044117
+#> 9 0.9849566
+#> 10 0.8160867
+#> 11 1.0428953
+#> 12 1.2109173
+#> 13 1.2522875
+#> 14 0.9418246
+#> 15 1.2547334
+#> 16 0.9979166
+#> 17 0.9698422
+#> 18 1.0053576
+#> 19 0.6291541
+#> 20 1.2222669
+#> 21 0.9392156
+#> 22 0.8618371
+#> 23 1.3905270
+#> 24 1.1287561
+#> 25 0.9480208
+#> 26 0.8805146
+#> 27 0.7944735
+#> 28 0.9337551
+#> 29 0.9913943
+#> 30 1.2030402
+#> 31 0.7667815
+#> 32 0.9314748
+#> 33 1.0526602
+#> 34 1.1869445
+#> 35 0.6727318
+#> 36 1.0244407
+#> 37 0.9559873
+#> 38 1.2306963
+#>
#Example 1 - using these_sample_ids parameter
#subset on FL cases with QC metrics available and plot
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
kridel_fl = dplyr::filter(metadata, pathology == "FL",
cohort == "FL_Kridel")
-#> Error in dplyr::filter(metadata, pathology == "FL", cohort == "FL_Kridel"): object 'metadata' not found
kridel_fl_samples = dplyr::select(kridel_fl, sample_id)
-#> Error in dplyr::select(kridel_fl, sample_id): object 'kridel_fl' not found
fancy_alignment_plot(these_sample_ids = kridel_fl_samples)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: Width not defined
+#> ℹ Set with `position_dodge(width = ...)`
+
#Example 2 - using already filtered metadata (these_samples_metadata)
fancy_alignment_plot(these_samples_metadata = kridel_fl)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: Width not defined
+#> ℹ Set with `position_dodge(width = ...)`
+
#Example 3 - using in-house metadata filtering options
fancy_alignment_plot(keep_cohort = "FL_Kridel",
keep_pathology = "FL")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: The melt generic in data.table has been passed a tbl_df and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(.). In the next version, this warning will become an error.
+#> Warning: Width not defined
+#> ℹ Set with `position_dodge(width = ...)`
+
#Return a plot for one sample, with default parameters.
fancy_cnbar(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> restricting to non-ICGC data
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist.
+#> Warning: Ignoring unknown aesthetics: label
+
diff --git a/docs/reference/fancy_multisamp_ideogram-1.png b/docs/reference/fancy_multisamp_ideogram-1.png
index 8ee17104..ea8aba83 100644
Binary files a/docs/reference/fancy_multisamp_ideogram-1.png and b/docs/reference/fancy_multisamp_ideogram-1.png differ
diff --git a/docs/reference/fancy_multisamp_ideogram.html b/docs/reference/fancy_multisamp_ideogram.html
index 91e3a36d..0c6f64e3 100644
--- a/docs/reference/fancy_multisamp_ideogram.html
+++ b/docs/reference/fancy_multisamp_ideogram.html
@@ -193,11 +193,47 @@ 
diff --git a/docs/reference/fancy_propcov_plot.html b/docs/reference/fancy_propcov_plot.html
index 6ebd6bf9..6fbbab2f 100644
--- a/docs/reference/fancy_propcov_plot.html
+++ b/docs/reference/fancy_propcov_plot.html
@@ -167,32 +167,34 @@ #Example 1 - using these_sample_ids parameter
#subset on FL cases with QC metrics available and plot
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
kridel_fl = dplyr::filter(metadata, pathology == "FL",
cohort == "FL_Kridel")
-#> Error in dplyr::filter(metadata, pathology == "FL", cohort == "FL_Kridel"): object 'metadata' not found
kridel_fl_samples = dplyr::select(kridel_fl, sample_id)
-#> Error in dplyr::select(kridel_fl, sample_id): object 'kridel_fl' not found
fancy_propcov_plot(these_sample_ids = kridel_fl_samples)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
+#> ℹ Please use the `fun` argument instead.
+#> ℹ The deprecated feature was likely used in the GAMBLR package.
+#> Please report the issue to the authors.
+#> Warning: Removed 20 rows containing missing values (`geom_violin()`).
+
#Example 2 - using already filtered metadata (these_samples_metadata)
fancy_propcov_plot(these_samples_metadata = kridel_fl)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: Removed 20 rows containing missing values (`geom_violin()`).
+
#Example 3 - using in-house metadata filtering options
fancy_propcov_plot(keep_cohort = "FL_Kridel",
keep_pathology = "FL")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Warning: Removed 20 rows containing missing values (`geom_violin()`).
+
diff --git a/docs/reference/fancy_qc_plot-1.png b/docs/reference/fancy_qc_plot-1.png
index 931bb97d..9e62c999 100644
Binary files a/docs/reference/fancy_qc_plot-1.png and b/docs/reference/fancy_qc_plot-1.png differ
diff --git a/docs/reference/fancy_qc_plot-2.png b/docs/reference/fancy_qc_plot-2.png
index 931bb97d..9e62c999 100644
Binary files a/docs/reference/fancy_qc_plot-2.png and b/docs/reference/fancy_qc_plot-2.png differ
diff --git a/docs/reference/fancy_qc_plot.html b/docs/reference/fancy_qc_plot.html
index 17a6743b..3eb19660 100644
--- a/docs/reference/fancy_qc_plot.html
+++ b/docs/reference/fancy_qc_plot.html
@@ -8,7 +8,7 @@
gtag('js', new Date());
gtag('config', 'UA-12345678-0');
-
+
#Example 1 - using these_sample_ids parameter
#subset on FL cases with QC metrics available and plot
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
kridel_fl = dplyr::filter(metadata, pathology == "FL",
cohort == "FL_Kridel")
-#> Error in dplyr::filter(metadata, pathology == "FL", cohort == "FL_Kridel"): object 'metadata' not found
kridel_fl_samples = dplyr::select(kridel_fl, sample_id)
-#> Error in dplyr::select(kridel_fl, sample_id): object 'kridel_fl' not found
fancy_qc_plot(these_sample_ids = kridel_fl_samples,
plot_data = "AverageBaseQuality",
y_axis_lab = "Average Base Quality",
plot_title = "Average Base Quality For FL_Kridel")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Joining with `by = join_by(sample_id, patient_id, biopsy_id)`
+
#Example 2 - using already filtered metadata (these_samples_metadata)
fancy_qc_plot(these_samples_metadata = kridel_fl,
@@ -225,19 +221,21 @@ Examples
plot_data = "AverageBaseQuality",
y_axis_lab = "Average Base Quality",
plot_title = "Average Base Quality For FL_Kridel")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
-
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Joining with `by = join_by(sample_id, patient_id, biopsy_id)`
+
+
#Example 3 - using in-house metadata filtering options
fancy_qc_plot(keep_cohort = "FL_Kridel",
keep_pathology = "FL",
plot_data = "AverageBaseQuality",
y_axis_lab = "Average Base Quality",
plot_title = "Average Base Quality For FL_Kridel")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> QC Metric successfully retreived for 56 samples out of a total of 56 samples in input sample table.
+#> Joining with `by = join_by(sample_id, patient_id, biopsy_id)`
+
#plot SNVs
fancy_snv_chrdistplot(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+#> Warning: Removed 1 rows containing missing values (`position_stack()`).
+
#plot SNVs and DNPs
fancy_snv_chrdistplot(this_sample_id = "HTMCP-01-06-00422-01A-01D",
include_dnp = TRUE,
plot_subtitle = "SNV + DNP Distribution Per Chromosome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+#> Warning: Removed 2 rows containing missing values (`position_stack()`).
+
#build plot sith default parameters
fancy_sv_sizedens(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> Warning: number of columns of result is not a multiple of vector length (arg 3)
+
#restrict plot to only chromosome 1 and 2
fancy_sv_sizedens(this_sample_id = "HTMCP-01-06-00422-01A-01D",
size_cutoff = 0,
chr_select = c("chr1", "chr2"))
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> Warning: number of columns of result is not a multiple of vector length (arg 3)
+
#plot ssm
fancy_v_chrcount(this_sample_id = "HTMCP-01-06-00422-01A-01D",
ssm = TRUE)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+#> Warning: Removed 2 rows containing missing values (`position_stack()`).
+
#plot SVs for chr 1-5
fancy_v_chrcount(this_sample_id = "HTMCP-01-06-00422-01A-01D",
@@ -230,10 +231,9 @@ Examples
projection = "grch37",
chr_select = paste0("chr", c(1:5)),
plot_subtitle = "SV Count Distribution (chr1-5)")
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> Warning: number of columns of result is not a multiple of vector length (arg 3)
+#> Warning: Removed 18 rows containing missing values (`position_stack()`).
+
#count all variants for one sample (default parameters)
fancy_v_count(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+
#count and plot all variants on chromosome 1
fancy_v_count(this_sample_id = "HTMCP-01-06-00422-01A-01D",
chr_select = c("chr1"))
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+
#plot SSM size distributions:
fancy_v_sizedis(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> trying to find output from: battenberg
+#> looking for flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--projection/HTMCP-01-06-00422-01A-01D--HTMCP-01-06-00422-10A-01D--matched.battenberg.grch37.seg
+
file_details_manta = find_files_extract_wildcards(tool_name = "manta",
genome_build = c("hg38", "grch37"),
search_pattern = ".bed")
-#> Error in dplyr::rename(., tumour_sample_id = `sample_id-1`, normal_sample_id = `sample_id-2`): Can't rename columns that don't exist.
-#> ✖ Column `sample_id-1` doesn't exist.
#get metadata
this_metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#get myc region
myc_region = gene_to_region(gene_symbol = "MYC",
@@ -183,11 +180,7 @@ Examples
region = myc_region,
type = "loss",
crop_distance = 100000000)
-#> restricting to non-ICGC data
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist.
+
#get all ssm in the MYC aSHM region
myc_ashm_maf = get_ssm_by_region(region = "8:128748352-128749427")
-#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.maf.bgz"
-#> Error in get_ssm_by_region(region = "8:128748352-128749427"): failed to find the file needed for this
#get mutations with 100 bp padding (default)
maf = genome_to_exome(maf = myc_ashm_maf)
-#> Error in genome_to_exome(maf = myc_ashm_maf): object 'myc_ashm_maf' not found
#get mutations covered in WEX with no padding
maf = genome_to_exome(maf = myc_ashm_maf,
padding = 0)
-#> Error in genome_to_exome(maf = myc_ashm_maf, padding = 0): object 'myc_ashm_maf' not found
#example 1, using a sample ID
bam_details = get_bams(this_sample_id = "HTMCP-01-06-00422-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(i = "In argument: `seq_type %in% seq_type_filter & tissue_status == \"normal\"`."), trace = structure(list(call = list(pkgdown::build_reference(lazy = TRUE), purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, examples_env = examples_env, run_dont_run = run_dont_run), map_("list", .x, .f, ..., .progress = .progress), with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)), withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } }), call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i), .f(.x[[i]], ...), withCallingHandlers(data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), error = function(err) { msg <- c(paste0("Failed to parse Rd in ", topic$file_in), i = err$message) abort(msg, parent = err) }), data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), run_examples(tags$tag_examples[[1]], env = if (is.null(examples_env)) NULL else new.env(parent = examples_env), topic = tools::file_path_sans_ext(topic$file_in), run_dont_run = run_dont_run), highlight_examples(code, topic, env = env), downlit::evaluate_and_highlight(code, fig_save = fig_save_topic, env = child_env(env), output_handler = evaluate::new_output_handler(value = pkgdown_print)), evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler), evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing), timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)), try(f, silent = TRUE), tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler), withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), eval_with_user_handlers(expr, envir, enclos, user_handlers), eval(expr, envir, enclos), eval(expr, envir, enclos), get_bams(this_sample_id = "HTMCP-01-06-00422-01A-01D"), get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter), sample_meta %>% dplyr::filter(seq_type %in% seq_type_filter & tissue_status == "normal") %>% dplyr::select(patient_id, sample_id, seq_type, genome_build) %>% as.data.frame() %>% dplyr::rename(normal_sample_id = "sample_id"), dplyr::rename(., normal_sample_id = "sample_id"), as.data.frame(.), dplyr::select(., patient_id, sample_id, seq_type, genome_build), dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter.data.frame(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter_rows(.data, dots, by), filter_eval(dots, mask = mask, error_call = error_call, user_env = user_env), withCallingHandlers(mask$eval_all_filter(dots, env_filter), error = dplyr_error_handler(dots = dots, mask = mask, bullets = filter_bullets, error_call = error_call), warning = function(cnd) { local_error_context(dots, i, mask) warning_handler(cnd) }, `dplyr:::signal_filter_one_column_matrix` = function(e) { warn_filter_one_column_matrix(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_across` = function(e) { warn_filter_across(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_data_frame` = function(e) { warn_filter_data_frame(env = error_call, user_env = user_env) }), mask$eval_all_filter(dots, env_filter), eval(), seq_type %in% seq_type_filter, .handleSimpleError(`<fn>`, "object 'seq_type_filter' not found", base::quote(seq_type %in% seq_type_filter)), h(simpleError(msg, call)), .handleSimpleError(`<fn>`, "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", base::quote(h(simpleError(msg, call)))), h(simpleError(msg, call)), abort(message, class = error_class, parent = parent, call = error_call)), parent = c(0L, 1L, 2L, 3L, 4L, 3L, 3L, 7L, 7L, 9L, 10L, 11L, 12L, 13L, 14L, 14L, 16L, 17L, 18L, 19L, 20L, 14L, 14L, 14L, 24L, 25L, 26L, 27L, 28L, 0L, 0L, 0L, 0L, 0L, 34L, 35L, 36L, 36L, 38L, 0L, 0L, 41L, 0L, 43L, 44L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("pkgdown", "purrr", "purrr", "purrr", "base", "purrr", "pkgdown", "base", "pkgdown", "pkgdown", "pkgdown", "downlit", "evaluate", "evaluate", "evaluate", "evaluate", "base", "base", "base", "base", "base", "base", "base", "evaluate", "base", "base", "GAMBLR", "GAMBLR", NA, "dplyr", "BiocGenerics", "dplyr", "dplyr", "dplyr", "dplyr", "dplyr", "base", NA, "dplyr", NA, "base", "base", "base", "dplyr", "rlang"), scope = c("::", "::", ":::", ":::", "::", ":::", "local", "::", ":::", ":::", ":::", "::", "::", ":::", "local", "local", "::", "::", "local", "local", "local", "::", "::", ":::", "::", "::", "::", "::", NA, "::", "::", "::", "::", ":::", ":::", ":::", "::", NA, "local", NA, "::", "local", "::", "local", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -45L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = structure(list( message = "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", call = h(simpleError(msg, call))), class = c("simpleError", "error", "condition")), rlang = list(inherit = TRUE), call = dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), use_cli_format = TRUE), class = c("rlang_error", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': ℹ In argument: `seq_type %in% seq_type_filter & tissue_status ==
+#> "normal"`.
+#> Caused by error in `h()`:
+#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found
#example 2, using a patient ID
bam_details = get_bams(this_patient_id = "HTMCP-01-06-00422")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(i = "In argument: `seq_type %in% seq_type_filter & tissue_status == \"normal\"`."), trace = structure(list(call = list(pkgdown::build_reference(lazy = TRUE), purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, examples_env = examples_env, run_dont_run = run_dont_run), map_("list", .x, .f, ..., .progress = .progress), with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)), withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } }), call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i), .f(.x[[i]], ...), withCallingHandlers(data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), error = function(err) { msg <- c(paste0("Failed to parse Rd in ", topic$file_in), i = err$message) abort(msg, parent = err) }), data_reference_topic(topic, pkg, examples_env = examples_env, run_dont_run = run_dont_run), run_examples(tags$tag_examples[[1]], env = if (is.null(examples_env)) NULL else new.env(parent = examples_env), topic = tools::file_path_sans_ext(topic$file_in), run_dont_run = run_dont_run), highlight_examples(code, topic, env = env), downlit::evaluate_and_highlight(code, fig_save = fig_save_topic, env = child_env(env), output_handler = evaluate::new_output_handler(value = pkgdown_print)), evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler), evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing), timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)), try(f, silent = TRUE), tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr), name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler), withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), eval_with_user_handlers(expr, envir, enclos, user_handlers), eval(expr, envir, enclos), eval(expr, envir, enclos), get_bams(this_patient_id = "HTMCP-01-06-00422"), get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter), sample_meta %>% dplyr::filter(seq_type %in% seq_type_filter & tissue_status == "normal") %>% dplyr::select(patient_id, sample_id, seq_type, genome_build) %>% as.data.frame() %>% dplyr::rename(normal_sample_id = "sample_id"), dplyr::rename(., normal_sample_id = "sample_id"), as.data.frame(.), dplyr::select(., patient_id, sample_id, seq_type, genome_build), dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter.data.frame(., seq_type %in% seq_type_filter & tissue_status == "normal"), filter_rows(.data, dots, by), filter_eval(dots, mask = mask, error_call = error_call, user_env = user_env), withCallingHandlers(mask$eval_all_filter(dots, env_filter), error = dplyr_error_handler(dots = dots, mask = mask, bullets = filter_bullets, error_call = error_call), warning = function(cnd) { local_error_context(dots, i, mask) warning_handler(cnd) }, `dplyr:::signal_filter_one_column_matrix` = function(e) { warn_filter_one_column_matrix(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_across` = function(e) { warn_filter_across(env = error_call, user_env = user_env) }, `dplyr:::signal_filter_data_frame` = function(e) { warn_filter_data_frame(env = error_call, user_env = user_env) }), mask$eval_all_filter(dots, env_filter), eval(), seq_type %in% seq_type_filter, .handleSimpleError(`<fn>`, "object 'seq_type_filter' not found", base::quote(get_gambl_metadata(tissue_status_filter = c("tumour", "normal"), seq_type_filter = seq_type_filter))), h(simpleError(msg, call)), .handleSimpleError(`<fn>`, "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", base::quote(h(simpleError(msg, call)))), h(simpleError(msg, call)), abort(message, class = error_class, parent = parent, call = error_call)), parent = c(0L, 1L, 2L, 3L, 4L, 3L, 3L, 7L, 7L, 9L, 10L, 11L, 12L, 13L, 14L, 14L, 16L, 17L, 18L, 19L, 20L, 14L, 14L, 14L, 24L, 25L, 26L, 27L, 28L, 0L, 0L, 0L, 0L, 0L, 34L, 35L, 36L, 36L, 38L, 0L, 0L, 41L, 0L, 43L, 44L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("pkgdown", "purrr", "purrr", "purrr", "base", "purrr", "pkgdown", "base", "pkgdown", "pkgdown", "pkgdown", "downlit", "evaluate", "evaluate", "evaluate", "evaluate", "base", "base", "base", "base", "base", "base", "base", "evaluate", "base", "base", "GAMBLR", "GAMBLR", NA, "dplyr", "BiocGenerics", "dplyr", "dplyr", "dplyr", "dplyr", "dplyr", "base", NA, "dplyr", NA, "base", "base", "base", "dplyr", "rlang"), scope = c("::", "::", ":::", ":::", "::", ":::", "local", "::", ":::", ":::", ":::", "::", "::", ":::", "local", "local", "::", "::", "local", "local", "local", "::", "::", ":::", "::", "::", "::", "::", NA, "::", "::", "::", "::", ":::", ":::", ":::", "::", NA, "local", NA, "::", "local", "::", "local", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)), row.names = c(NA, -45L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = structure(list( message = "error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found", call = h(simpleError(msg, call))), class = c("simpleError", "error", "condition")), rlang = list(inherit = TRUE), call = dplyr::filter(., seq_type %in% seq_type_filter & tissue_status == "normal"), use_cli_format = TRUE), class = c("rlang_error", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': ℹ In argument: `seq_type %in% seq_type_filter & tissue_status ==
+#> "normal"`.
+#> Caused by error in `h()`:
+#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'seq_type_filter' not found
#basic usage, generic lymphoma gene list
cn_matrix = get_cn_states(regions_bed=grch37_lymphoma_genes_bed)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
myc_region <- gene_to_region(
gene_symbol = "MYC",
@@ -173,9 +170,6 @@ Examples
regions_list = myc_region,
region_names = "MYC"
)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
# For capture
single_gene_cn <- get_cn_states(
@@ -183,9 +177,6 @@ Examples
region_names = "MYC",
this_seq_type = "capture"
)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#basic usage
maf_data = get_coding_ssm(seq_type = "genome", limit_cohort = c("BL_ICGC"))
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 17 samples
maf_data = get_coding_ssm(seq_type = "genome", limit_samples = "HTMCP-01-06-00485-01A-01D")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 1 samples
coding_tabulated_df = get_coding_ssm_status(maf_data = grande_maf,
gene_symbols = "EGFR")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Joining with `by = join_by(sample_id)`
+#> Adding missing grouping variables: `SYMBOL`
+#> Adding missing grouping variables: `SYMBOL`
+#> annotating hotspots
+#> Joining with `by = join_by(sample_id)`
+#> FOXO1HOTSPOT
#all lymphoma genes from bundled NHL gene list
coding_tabulated_df = get_coding_ssm_status()
#> defaulting to all lymphoma genes
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 1646 samples
+#> Joining with `by = join_by(sample_id)`
+#> Adding missing grouping variables: `SYMBOL`
+#> Adding missing grouping variables: `SYMBOL`
+#> annotating hotspots
+#> Joining with `by = join_by(sample_id)`
+#> FOXO1HOTSPOT
+#> OK
+#> CREBBPHOTSPOT
+#> OK
+#> MYD88HOTSPOT
+#> OK
get_combined_sv(oncogenes = c("MYC", "BCL2", "BCL6"))
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> # A tibble: 17,573 × 20
+#> CHROM_A START_A END_A CHROM_B START_B END_B manta_name SCORE STRAND_A
+#> <chr> <dbl> <dbl> <chr> <dbl> <dbl> <chr> <dbl> <chr>
+#> 1 14 106325575 106325579 8 1.29e8 1.29e8 MantaBND:… NA +
+#> 2 14 106325996 106325998 8 1.29e8 1.29e8 MantaBND:… NA -
+#> 3 14 106211834 106211836 8 1.29e8 1.29e8 MantaBND:… NA -
+#> 4 14 106324104 106324108 8 1.29e8 1.29e8 MantaBND:… NA +
+#> 5 14 106326646 106326649 8 1.29e8 1.29e8 MantaBND:… NA -
+#> 6 14 106330376 106330685 8 1.29e8 1.29e8 MantaBND:… NA +
+#> 7 14 106329932 106329935 8 1.29e8 1.29e8 MantaBND:… NA +
+#> 8 14 106329938 106329940 8 1.29e8 1.29e8 MantaBND:… NA -
+#> 9 18 60368230 60368530 3 1.83e8 1.83e8 MantaBND:… NA +
+#> 10 22 23247400 23247402 8 1.29e8 1.29e8 MantaBND:… NA -
+#> # ℹ 17,563 more rows
+#> # ℹ 11 more variables: STRAND_B <chr>, tumour_sample_id <chr>,
+#> # normal_sample_id <chr>, VAF_tumour <dbl>, DP <dbl>, gridss_name <chr>,
+#> # ANNOTATION_A <chr>, DIST_TO_ANNOTATION_A <dbl>, ANNOTATION_B <chr>,
+#> # DIST_TO_ANNOTATION_B <dbl>, FILTER <chr>
excluded_samp = get_excluded_samples()
-#> [1] "missing: /Users/rmorin/git/gambl/config/exclude.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/config/exclude.tsv' does not exist.
#basic usage
my_metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#use pre-defined custom sample sets
only_blgsp_metadata = get_gambl_metadata(case_set = "BLGSP-study")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#override default filters and request metadata for samples other than tumour genomes,
#e.g. also get the normals
only_normal_metadata = get_gambl_metadata(tissue_status_filter = c('tumour','normal'))
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
non_duplicated_genome_and_capture = get_gambl_metadata(seq_type_filter = c('genome', 'capture'),
seq_type_priority = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
get_gambl_outcomes.RdGet the patient-centric clinical metadata.
-get_gambl_outcomes(
- patient_ids,
- time_unit = "year",
- censor_cbioportal = FALSE,
- complete_missing = FALSE,
- from_flatfile = TRUE
-)Vector of patient IDs.
Return follow-up times in one of three time units: year, month or day. Default is "year".
Optionally request the censoring to be encoded in the specific style required by cBioPortal. Default is FALSE.
Optionally fill in any gaps to ensure we have values for every patient (censor at 0 if missing). Default is FALSE.
Optionally set to FALSE to use the database to get the survival data. Default is TRUE.
Data frame with one row for each patient_id.
-INTERNAL FUNCTION called by get_gambl_metadata, not meant for out-of-package usage.
outcome_df = get_gambl_outcomes()
-#> Error in get_gambl_outcomes(): could not find function "get_gambl_outcomes"
-
-MYC_cn_expression = get_gene_cn_and_expression("MYC")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> [1] "grep -w -F -e Hugo_Symbol -e MYC /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv"
MYC_expr = get_gene_expression(hugo_symbols = c("MYC"), join_with = "mrna")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> [1] "grep -w -F -e Hugo_Symbol -e MYC /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv"
#Read full expression values df (no subsetting on genes)
full_expression_df = get_gene_expression(all_genes = TRUE,
join_with = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Warning: NAs produced by integer overflow
+#> Error in vec_init(value, nrow * ncol): `n` must be a single number, not an integer `NA`.
#Use loaded df (in the previous step) to get expression values for IRF4 and MYC.
irf4_myc_expressions = get_gene_expression(hugo_symbols = c("IRF4", "MYC"),
@@ -175,9 +172,7 @@ Examples
join_with = "genome",
from_flatfile = FALSE,
expression_data = full_expression_df)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': object 'full_expression_df' not found
#lazily get every SV in the table with default quality filters
all_sv = get_manta_sv(verbose = FALSE)
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> WARNING! No SV calls found in flat-file for: 171116-PL02
+#> WARNING! No SV calls found in flat-file for: 171447-PL01
+#> WARNING! No SV calls found in flat-file for: 171451-PL01
#get all SVs for a single sample
some_sv = get_manta_sv(these_sample_ids = "94-15772_tumorA")
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
#get the SVs in a region around MYC
myc_locus_sv = get_manta_sv(region = "8:128723128-128774067", verbose = FALSE)
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> WARNING! No SV calls found in flat-file for: 171116-PL02
+#> WARNING! No SV calls found in flat-file for: 171447-PL01
+#> WARNING! No SV calls found in flat-file for: 171451-PL01
#get SVs for multiple samples, using these_samples_id
my_metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
these_samples = dplyr::select(my_metadata, sample_id)
-#> Error in dplyr::select(my_metadata, sample_id): object 'my_metadata' not found
my_samples_df = head(these_samples, 10)
-#> Error in head(these_samples, 10): object 'these_samples' not found
my_samples = pull(my_samples_df, sample_id)
-#> Error in pull(my_samples_df, sample_id): could not find function "pull"
my_svs_2 = get_manta_sv(these_sample_ids = my_samples,
projection = "hg38",
verbose = FALSE)
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
#get SVs for multiple samples using a metadata table and with no VAF/score filtering
my_metadata = get_gambl_metadata() %>%
this_metadata = head(my_metadata, 10)
-#> Error in head(my_metadata, 10): object 'my_metadata' not found
+#> Error in get_gambl_metadata() %>% this_metadata = head(my_metadata, 10): invalid (NULL) left side of assignment
my_svs = get_manta_sv(these_samples_metadata = this_metadata,
verbose = FALSE,
min_vaf = 0,
min_score = 0)
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> Error in get_manta_sv(these_samples_metadata = this_metadata, verbose = FALSE, min_vaf = 0, min_score = 0): object 'this_metadata' not found
all_sv = get_manta_sv()
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> Reading 01-16433_tumorC from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/01-16433_tumorC--01-16433_normal--matched.somaticSV.bedpe
+#> Reading 012-02-1TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-02-1TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-11-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-11-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-13-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-13-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-15-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-15-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-16-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-16-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-17-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-17-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-18-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-18-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 012-19-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/012-19-01TD--012-0034-01ND--matched.somaticSV.bedpe
+#> Reading 019-0047-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-0047-01TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 019-05-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-05-01TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 019-12-02TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-12-02TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 019-15-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-15-01TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 019-18-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-18-01TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 019-19-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/019-19-01TD--019-0048-01ND--matched.somaticSV.bedpe
+#> Reading 02-11368_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/02-11368_tumorB--02-11368_normal--matched.somaticSV.bedpe
+#> Reading 02-15745_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/02-15745_tumorA--02-15745_normal--matched.somaticSV.bedpe
+#> Reading 02-15745_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/02-15745_tumorB--02-15745_normal--matched.somaticSV.bedpe
+#> Reading 02-15745_tumorC from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/02-15745_tumorC--02-15745_normal--matched.somaticSV.bedpe
+#> Reading 03-24364_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/03-24364_tumorA--03-24364_normal--matched.somaticSV.bedpe
+#> Reading 03-28283_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/03-28283_tumorB--03-28283_normal--matched.somaticSV.bedpe
+#> Reading 05-11115_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11115_tumorA--05-11115_normal--matched.somaticSV.bedpe
+#> Reading 05-11115_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11115_tumorB--05-11115_normal--matched.somaticSV.bedpe
+#> Reading 05-11115_tumorC from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11115_tumorC--05-11115_normal--matched.somaticSV.bedpe
+#> Reading 05-11115_tumorD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11115_tumorD--05-11115_normal--matched.somaticSV.bedpe
+#> Reading 05-11115_tumorE from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11115_tumorE--05-11115_normal--matched.somaticSV.bedpe
+#> Reading 05-11725_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-11725_tumorB--05-11725_normal--matched.somaticSV.bedpe
+#> Reading 05-15635_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-15635_tumorA--05-15635_normal--matched.somaticSV.bedpe
+#> Reading 05-15635_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-15635_tumorB--05-15635_normal--matched.somaticSV.bedpe
+#> Reading 05-27675_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-27675_tumorA--05-27675_normal--matched.somaticSV.bedpe
+#> Reading 05-28753_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-28753_tumorA--05-28753N--matched.somaticSV.bedpe
+#> Reading 05-28753_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-28753_tumorB--05-28753N--matched.somaticSV.bedpe
+#> Reading 05-28753_tumorC from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/05-28753_tumorC--05-28753N--matched.somaticSV.bedpe
+#> Reading 06-28477_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/06-28477_tumorA--FL2002N--matched.somaticSV.bedpe
+#> Reading 063-0127-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/063-0127-01TD--063-0126-02ND--matched.somaticSV.bedpe
+#> Reading 063-02-1TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/063-02-1TD--063-0126-02ND--matched.somaticSV.bedpe
+#> Reading 063-08-04BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/063-08-04BD--063-0126-02ND--matched.somaticSV.bedpe
+#> Reading 063-09-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/063-09-01TD--063-0126-02ND--matched.somaticSV.bedpe
+#> Reading 08-26563_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/08-26563_tumorA--08-26563_normal--matched.somaticSV.bedpe
+#> Reading 09-15148_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/09-15148_tumorB--09-15148_normal--matched.somaticSV.bedpe
+#> Reading 09-31601_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/09-31601_tumorB--09-31601_normal--matched.somaticSV.bedpe
+#> Reading 10-13016_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/10-13016_tumorA--10-13016_normal--matched.somaticSV.bedpe
+#> Reading 10-18191T from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/10-18191T--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 102-01-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/102-01-01TD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 102-0202-1DVT from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/102-0202-1DVT--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 11-13204_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/11-13204_tumorB--11-13204_normal--matched.somaticSV.bedpe
+#> Reading 12-11721_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/12-11721_tumorB--12-11721_normal--matched.somaticSV.bedpe
+#> Reading 12-38161_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/12-38161_tumorA--12-38161_normal--matched.somaticSV.bedpe
+#> Reading 13-27960_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/13-27960_tumorB--13-27960N--matched.somaticSV.bedpe
+#> Reading 13-27975_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/13-27975_tumorA--13-27975_normal--matched.somaticSV.bedpe
+#> Reading 13-27975_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/13-27975_tumorB--13-27975_normal--matched.somaticSV.bedpe
+#> Reading 13F44-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/13F44-PL02--13089-DNA01--matched.somaticSV.bedpe
+#> Reading 13I80-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/13I80-PL02--13575-DNA01--matched.somaticSV.bedpe
+#> Reading 13N66-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/13N66-PL01--13G42-DNAGL01--matched.somaticSV.bedpe
+#> Reading 14-11465_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/14-11465_tumorB--14-11465_normal--matched.somaticSV.bedpe
+#> Reading 14-11777_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/14-11777_tumorB--14-11777N--matched.somaticSV.bedpe
+#> Reading 14-26768_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/14-26768_tumorA--14-26768_normal--matched.somaticSV.bedpe
+#> Reading 140127-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/140127-PL02--13430-GL-DNA--matched.somaticSV.bedpe
+#> Reading 141498-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/141498-PL01--13C53-DNAGL02--matched.somaticSV.bedpe
+#> Reading 141900-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/141900-PL01--141666-BC01--matched.somaticSV.bedpe
+#> Reading 150327-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/150327-PL02--13F62-BC01--matched.somaticSV.bedpe
+#> Reading 1523-01-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/1523-01-01TD--1523-04-01ND--matched.somaticSV.bedpe
+#> Reading 1523-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/1523-03-01BD--1523-04-01ND--matched.somaticSV.bedpe
+#> Reading 1563-01-03TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/1563-01-03TD--1563-01-01ND--matched.somaticSV.bedpe
+#> Reading 1563-02-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/1563-02-01BD--1563-01-01ND--matched.somaticSV.bedpe
+#> Reading 160745-PL04 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/160745-PL04--160942-BC01--matched.somaticSV.bedpe
+#> Reading 161135-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/161135-PL02--160942-BC01--matched.somaticSV.bedpe
+#> Reading 161396-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/161396-PL02--160942-BC01--matched.somaticSV.bedpe
+#> Reading 161402-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/161402-PL02--140928-BC01--matched.somaticSV.bedpe
+#> Reading 1669-04-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/1669-04-01BD--1669-02-01ND--matched.somaticSV.bedpe
+#> Reading 170867-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/170867-PL02--170458-BC01--matched.somaticSV.bedpe
+#> Reading 171116-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/171116-PL02--170484-CS01--matched.somaticSV.bedpe
+#> WARNING! No SV calls found in flat-file for: 171116-PL02
+#> Reading 171290-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/171290-PL01--170458-BC01--matched.somaticSV.bedpe
+#> Reading 171414-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/171414-PL02--171241-BC01--matched.somaticSV.bedpe
+#> Reading 171447-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/171447-PL01--190142-DNAGL02--matched.somaticSV.bedpe
+#> WARNING! No SV calls found in flat-file for: 171447-PL01
+#> Reading 171451-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/171451-PL01--171328-BC01--matched.somaticSV.bedpe
+#> WARNING! No SV calls found in flat-file for: 171451-PL01
+#> Reading 180204-PL01-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/180204-PL01-PL02--171364-BC01--matched.somaticSV.bedpe
+#> Reading 180445-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/180445-PL02--171241-BC01--matched.somaticSV.bedpe
+#> Reading 180840-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/180840-PL01--180840-CS01--matched.somaticSV.bedpe
+#> Reading 181712-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/181712-PL01--181677-BC01--matched.somaticSV.bedpe
+#> Reading 190017-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/190017-PL01--181510-CS01--matched.somaticSV.bedpe
+#> Reading 190128-PL01-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/190128-PL01-PL02--161134-DNAGL02--matched.somaticSV.bedpe
+#> Reading 190806-PL01-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/190806-PL01-PL02--141055-DNAGL02--matched.somaticSV.bedpe
+#> Reading 191457-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/191457-PL02--190142-DNAGL02--matched.somaticSV.bedpe
+#> Reading 191510-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/191510-PL02--190263-BC01--matched.somaticSV.bedpe
+#> Reading 191621-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/191621-PL01--190906-CS01--matched.somaticSV.bedpe
+#> Reading 200836-PL01 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/200836-PL01--201151-BC01--matched.somaticSV.bedpe
+#> Reading 210541-PL02 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hg38/somaticSV/210541-PL02--211147-CS01--matched.somaticSV.bedpe
+#> Reading 3034-03-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3034-03-01TD--3034-01-01ND--matched.somaticSV.bedpe
+#> Reading 3034-04-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3034-04-01BD--3034-01-01ND--matched.somaticSV.bedpe
+#> Reading 3299-01-02TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3299-01-02TD--3299-02-03ND--matched.somaticSV.bedpe
+#> Reading 3299-02-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3299-02-01TD--3299-02-03ND--matched.somaticSV.bedpe
+#> Reading 3299-03-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3299-03-01TD--3299-02-03ND--matched.somaticSV.bedpe
+#> Reading 3299-04-1TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3299-04-1TD--3299-02-03ND--matched.somaticSV.bedpe
+#> Reading 3299-05-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3299-05-01TD--3299-02-03ND--matched.somaticSV.bedpe
+#> Reading 3495-02-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3495-02-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 3495-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/3495-03-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 365-11-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/365-11-01BD--365-01-01ND--matched.somaticSV.bedpe
+#> Reading 365-16-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/365-16-01TD--365-01-01ND--matched.somaticSV.bedpe
+#> Reading 365-1951-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/365-1951-01TD--365-01-01ND--matched.somaticSV.bedpe
+#> Reading 4675-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4675-03-01BD--4675-05-01ND--matched.somaticSV.bedpe
+#> Reading 4675-04-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4675-04-01BD--4675-05-01ND--matched.somaticSV.bedpe
+#> Reading 4676-02-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4676-02-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4686-02-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4686-02-01TD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4686-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4686-03-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4687-02-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4687-02-01TD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4687-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4687-03-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4690-02-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4690-02-01TD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 4690-03-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/4690-03-01BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 816-01-1TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/816-01-1TD--816-05-02ND--matched.somaticSV.bedpe
+#> Reading 816-06-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/816-06-01TD--816-05-02ND--matched.somaticSV.bedpe
+#> Reading 816-08-01TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/816-08-01TD--816-05-02ND--matched.somaticSV.bedpe
+#> Reading 835-01-02BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/835-01-02BD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 835-02-03TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/835-02-03TD--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 839-01-1TD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/839-01-1TD--839-03-1ND--matched.somaticSV.bedpe
+#> Reading 839-04-01BD from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/839-04-01BD--839-03-1ND--matched.somaticSV.bedpe
+#> Reading 97-28459_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/97-28459_tumorB--FL3006N--matched.somaticSV.bedpe
+#> Reading 98-28290T from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/98-28290T--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 98-30186_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/98-30186_tumorA--98-30186_normal--matched.somaticSV.bedpe
+#> Reading 99-25549T from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--hs37d5/somaticSV/99-25549T--14-11247Normal--unmatched.somaticSV.bedpe
+#> Reading 99-27783_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/99-27783_tumorA--99-27783_normal--matched.somaticSV.bedpe
+#> Reading 99-27783_tumorB from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/99-27783_tumorB--99-27783_normal--matched.somaticSV.bedpe
+#> Reading KM-H2 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/KM-H2--14-11247N--unmatched.somaticSV.bedpe
+#> Reading L-428 from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/L-428--14-11247N--unmatched.somaticSV.bedpe
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
missing_samples = dplyr::anti_join(metadata, all_sv, by = c("sample_id" = "tumour_sample_id"))
-#> Error in dplyr::anti_join(metadata, all_sv, by = c(sample_id = "tumour_sample_id")): object 'metadata' not found
missing_from_merge = get_manta_sv_by_samples(these_samples_metadata = missing_samples, verbose = FALSE)
-#> Error in pull(these_samples_metadata, sample_id): object 'missing_samples' not found
+#> WARNING! No SV calls found in flat-file for: 171116-PL02
+#> WARNING! No SV calls found in flat-file for: 171447-PL01
+#> WARNING! No SV calls found in flat-file for: 171451-PL01
#load metadata.
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
dlbcl_bl_meta = dplyr::filter(metadata, pathology %in% c("DLBCL", "BL"))
-#> Error in dplyr::filter(metadata, pathology %in% c("DLBCL", "BL")): object 'metadata' not found
#bring together all derived sample-level results from many GAMBL pipelines.
dlbcl_bl_meta = collate_results(join_with_full_metadata = TRUE,
these_samples_metadata = dlbcl_bl_meta)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> /projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
+#> Joining with `by = join_by(patient_id, sample_id, biopsy_id)`
#get ashm regions
some_regions = grch37_ashm_regions
diff --git a/docs/reference/get_sample_cn_segments.html b/docs/reference/get_sample_cn_segments.html
index 6ad78706..4b8d936c 100644
--- a/docs/reference/get_sample_cn_segments.html
+++ b/docs/reference/get_sample_cn_segments.html
@@ -167,32 +167,20 @@ Examples
#> Warning: cannot open file '../samples-test.csv': No such file or directory
#> Error in file(con, "r"): cannot open the connection
multiple_samples = get_sample_cn_segments(multiple_samples = TRUE, sample_list = sample_list)
-#> restricting to non-ICGC data
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist.
+#> Error in dplyr::filter(all_segs, ID %in% sample_list): ℹ In argument: `ID %in% sample_list`.
+#> Caused by error in `h()`:
+#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'sample_list' not found
#Return cn segments for multiple samples (provided as vector of sample IDs):
these_sample_list = c("00-15201_tumorA", "00-15201_tumorB")
samples = get_sample_cn_segments(multiple_samples = TRUE,
sample_list = these_sample_list)
-#> restricting to non-ICGC data
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/genome--projection/all--grch37.seg' does not exist.
# For capture
samples = get_sample_cn_segments(
multiple_samples = TRUE,
sample_list = these_sample_list,
this_seq_type = "capture"
)
-#> restricting to non-ICGC data
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/capture--projection/all--grch37.seg"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/cnv_master-1.0/99-outputs/capture--projection/all--grch37.seg' does not exist.
get_sample_wildcards(this_sample_id = "00-15201_tumorA",
seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> $tumour_sample_id
+#> [1] "00-15201_tumorA"
+#>
+#> $normal_sample_id
+#> [1] "00-15201_normal"
+#>
+#> $seq_type
+#> [1] "genome"
+#>
+#> $pairing_status
+#> [1] "matched"
+#>
+#> $genome_build
+#> [1] "grch37"
+#>
+#> $unix_group
+#> [1] "gambl"
+#>
my_session = get_ssh_session()
#> you should also run this command to ensure the ssh library is loaded:
#> library(ssh)
-#> Server fingerprint: c1:c2:a2:fe:bb:5b:c6:26:de:5d:db:46:d5:e6:1d:51:d1:e3:e9:b5
+#> Server fingerprint: 19:4c:16:92:e8:1b:9a:06:55:ef:4d:aa:24:fe:62:50:57:a6:aa:92
#basic usage
my_mutations = get_ssm_by_region(region = "chr8:128,723,128-128,774,067")
-#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.maf.bgz"
-#> Error in get_ssm_by_region(region = "chr8:128,723,128-128,774,067"): failed to find the file needed for this
#specifying chromosome, start and end individually
my_mutations = get_ssm_by_region(chromosome = "8",
qstart = 128723128,
qend = 128774067)
-#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.maf.bgz"
-#> Error in get_ssm_by_region(chromosome = "8", qstart = 128723128, qend = 128774067): failed to find the file needed for this
#keep all 116 columns in the read MAF
bcl2_all_details = get_ssm_by_region(region = "chr18:60796500-60988073",
basic_columns = FALSE)
-#> [1] "missing: /Users/rmorin/gambl_results/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.maf.bgz"
-#> Error in get_ssm_by_region(region = "chr18:60796500-60988073", basic_columns = FALSE): failed to find the file needed for this
+#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
+#> e.g.:
+#> dat <- vroom(...)
+#> problems(dat)
grch37_ashm_regions.RdASHM regions in respect to grch37.
-grch37_ashm_regionsgrch37_ashm_regionsA data frame with 88 rows and 7 columns.
The chromosome for which the region is residing on
start coordinate for the region
end coordinate for the region
Gene symbol (Hugo)
Region name
Regulatory element
gene-region format
hg38_ashm_regions.RdASHM regions in respect to hg38.
-hg38_ashm_regionshg38_ashm_regionsA data frame with 88 rows and 7 columns.
The chromosome for which the region is residing on
start coordinate for the region
end coordinate for the region
Gene symbol (Hugo)
Region name
Regulatory element
gene-region format
hg19_sv = get_manta_sv(verbose = FALSE)
-#> [1] "missing: /Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe"
-#> Cannot find file locally. If working remotely, perhaps you forgot to load your config (see below) or sync your files?
-#> Sys.setenv(R_CONFIG_ACTIVE = "remote")
-#> Error: '/Users/rmorin/gambl_results/gambl/svar_master-1.0/merges/gridss_manta.genome--grch37.bedpe' does not exist.
+#> WARNING! No SV calls found in flat-file for: 171116-PL02
+#> WARNING! No SV calls found in flat-file for: 171447-PL01
+#> WARNING! No SV calls found in flat-file for: 171451-PL01
hg19_sv = head(hg19_sv, 100)
-#> Error in head(hg19_sv, 100): object 'hg19_sv' not found
hg38_sv = liftover_bedpe(bedpe_df = hg19_sv,
target_build = "hg38")
-#> Error in liftover_bedpe(bedpe_df = hg19_sv, target_build = "hg38"): object 'hg19_sv' not found
+#> Discarding unchained sequences: chrhs37d5
lymphoma_genes.RdA data frame with known lymphoma genes, genes are annotated by pathology, as well as literature support.
-lymphoma_geneslymphoma_genesA data frame with 196 rows and 12 columns.
Gene symbol
Boolean flag annotating if the described genes are significant for the pathology (DLBCL)
Boolean flag annotating if the described genes are significant for the pathology (FL)
Boolean flag annotating if the described genes are significant for the pathology (BL)
Boolean flag annotating if the described genes are significant for the pathology (MCL)
Boolean flag annotating if the described genes are significant for the pathology (CLL)
Ensembl gene ID
Gene symbol (Hugo)
Boolean flag, TRUE if lymphGen
Boolean flag, TRUE if gene verified by the stated study (Reddy)
Boolean flag, TRUE if gene verified by the stated study (Chapuy)
Entrez ID for the described gene
map_metadata_to_colours.RdINTERNAL FUNCTION called by plot_sample_circos and get_mutation_frequency_bin_matrix, not meant for out-of-package usage. -Assign a colour palette to metadata columns automatically and consistently.
-map_metadata_to_colours(
- metadataColumns,
- these_samples_metadata,
- column_alias = list(),
- as_vector = TRUE,
- verbose = FALSE,
- annoAlpha = 1
-)Names of the metadata columns to assign colours for.
Metadata for just the samples you need colours for.
A list of column_names with values indicating what gambl colour scheme they should use (e.g. pos_neg, pathology, lymphgen).
Boolean statement that is set to TRUE per default.
Set to TRUE to enable verbose mode (debugging messages.
Optional alpha to apply to annotation colours.
Either a vector or list of colours.
-#get metadata
-all_meta = get_gambl_metadata()
-
-#get colours
-all_cols = map_metadata_to_colours(metadataColumns = c("lymphgen",
- "pathology",
- "genetic_subgroup"),
- these_samples_metadata = all_meta,
- column_alias = list("nothing" = "FL"),
- as_vector = F)
-#> Error in map_metadata_to_colours(metadataColumns = c("lymphgen", "pathology", "genetic_subgroup"), these_samples_metadata = all_meta, column_alias = list(nothing = "FL"), as_vector = F): could not find function "map_metadata_to_colours"
-
-plot_multi_timepoint.RdThis function doesn't do anything yet, thus, it's not currently exported to NAMESPACE.
-plot_multi_timepoint(
- mafs,
- this_sample_id,
- genes,
- show_noncoding = FALSE,
- detail
-)TODO
TODO
TODO
TODO
TODO
-internal
plot_mutation_dynamics_heatmap.RdPlot a heatmap comparing the VAF of mutations in T1/T2 pairs.
-plot_mutation_dynamics_heatmap(
- maf1,
- maf2,
- vafcolname,
- patient_colname = "patient_id",
- these_samples_metadata,
- sortByColumns,
- metadata_columns = c("sample_id"),
- gene_orientation = "bottom",
- annotate_zero = FALSE,
- genes,
- top_n_genes,
- drop_unless_lowvaf = FALSE,
- vaf_cutoff_to_drop = 0.05,
- cluster_columns = FALSE,
- cluster_rows = FALSE
-)Data frame of simple somatic mutations at time point A.
Data frame of simple somatic mutations at time point B.
Name of variable that holds VAF in maf. If not supplied, vaf will be calcualted.
Column name that holds patient name (default is "patient_id").
GAMBL metadata subset to the cases you want to process (or full metadata).
Which of the metadata to sort on for the heatmap.
A vector containing the categorical column names you want to plot below.
Where genes would be plotted. Default is "bottom".
Indicate a variant that had VAF = 0 in one of the two time points. Default is FALSE.
An optional vector of genes to restrict your plot to.
How many genes to be added to the plot.
Will drop some genes where VAF is low, default is FALSE.
Which VAF cut-off value to use when dropping variants before plotting.
Boolean statement for clustering by columns, defaults to FALSE.
Boolean statement for clustering by rows, defaults to FALSE.
Nothing
-Currently unfinished plotting function. Thus, I have removed it from export until it's in a state where it can be included in GAMBLR. -Parameter descriptions need to be updated so that the origin of the incoming data is clear. -Examples would also need to be added before this function gets exported into NAMESPACE.
-
diff --git a/docs/reference/populate_each_tool_result.html b/docs/reference/populate_each_tool_result.html
index bc3ac4cc..dd98ee47 100644
--- a/docs/reference/populate_each_tool_result.html
+++ b/docs/reference/populate_each_tool_result.html
@@ -144,9 +144,6 @@ tool_results = populate_each_tool_result("smlims_3", "grch37", "gambl", FALSE)
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
#get data for plotting
ssm = get_coding_ssm(limit_cohort = c("BL_Adult", "BL_Pediatric"), seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 219 samples
ssm = maftools::read.maf(ssm)
-#> Error in is.data.frame(x = maf): object 'ssm' not found
+#> -Validating
+#> -Silent variants: 10604
+#> -Summarizing
+#> -Processing clinical data
+#> --Missing clinical data
+#> -Finished in 3.529s elapsed (9.005s cpu)
meta = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
meta = dplyr::filter(meta, cohort %in% c("BL_Adult", "BL_Pediatric"))
-#> Error in dplyr::filter(meta, cohort %in% c("BL_Adult", "BL_Pediatric")): object 'meta' not found
#build plot
prettyCoOncoplot(maf = ssm,
@@ -198,7 +199,13 @@ Examples
legend_row = 2,
label1 = "Adult",
label2 = "Pediatric")
-#> Error in prettyCoOncoplot(maf = ssm, metadata = meta, comparison_column = "cohort", include_noncoding = NULL, minMutationPercent = 0, genes = c("MYC", "TET2", "TP53", "DDX3X", "ID3"), metadataColumns = c("pathology", "EBV_status_inf", "pairing_status", "cohort"), splitColumnName = "EBV_status_inf", metadataBarHeight = 10, fontSizeGene = 12, metadataBarFontsize = 10, legend_row = 2, label1 = "Adult", label2 = "Pediatric"): object 'meta' not found
+#> -Processing clinical data
+#> --Possible FLAGS among top ten genes:
+#> TTN
+#> -Processing clinical data
+#> [1] "numcases: 124"
+#> [1] "numgenes: 5"
+#> Error in gpar(fontsize = legendFontSize): could not find function "gpar"
metadata = get_gambl_metadata(case_set = "tFL-study")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Joining with `by = join_by(sample_id)`
+#> Joining with `by = join_by(sample_id)`
this_meta = dplyr::filter(metadata, pairing_status == "matched")
-#> Error in dplyr::filter(metadata, pairing_status == "matched"): object 'metadata' not found
this_meta = dplyr::filter(this_meta, consensus_pathology %in% c("FL", "DLBCL"))
-#> Error in dplyr::filter(this_meta, consensus_pathology %in% c("FL", "DLBCL")): object 'this_meta' not found
maf = get_coding_ssm(limit_samples = this_metadata$sample_id,
basic_columns = TRUE,
seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> Error in dplyr::filter(., sample_id %in% limit_samples): ℹ In argument: `sample_id %in% limit_samples`.
+#> Caused by error in `h()`:
+#> ! error in evaluating the argument 'table' in selecting a method for function '%in%': object 'this_metadata' not found
prettyForestPlot(maf = maf,
metadata = this_metadata,
diff --git a/docs/reference/prettyGeneCloud-1.png b/docs/reference/prettyGeneCloud-1.png
index 3a3346a1..0f33e23c 100644
Binary files a/docs/reference/prettyGeneCloud-1.png and b/docs/reference/prettyGeneCloud-1.png differ
diff --git a/docs/reference/prettyGeneCloud.html b/docs/reference/prettyGeneCloud.html
index 559d67ff..41437f21 100644
--- a/docs/reference/prettyGeneCloud.html
+++ b/docs/reference/prettyGeneCloud.html
@@ -153,21 +153,537 @@ Details
Examples
#get all coding SSM
maf = get_coding_ssm(seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 1646 samples
#get gene symbols from MAF
maf_genes = dplyr::filter(maf, Hugo_Symbol != "Unknown")
-#> Error in dplyr::filter(maf, Hugo_Symbol != "Unknown"): object 'maf' not found
maf_genes_chr1 = dplyr::filter(maf_genes, Chromosome == "1")
-#> Error in dplyr::filter(maf_genes, Chromosome == "1"): object 'maf_genes' not found
my_genes = maf_genes_chr1$Hugo_Symbol
-#> Error in eval(expr, envir, enclos): object 'maf_genes_chr1' not found
#build wordcloud
prettyGeneCloud(maf_df = maf, these_genes = my_genes)
-#> Error in dplyr::filter(maf_df, Hugo_Symbol %in% these_genes): object 'maf' not found
+#> Hugo_Symbol n
+#> 1 A3GALT2 4
+#> 2 AADACL3 6
+#> 3 AADACL4 7
+#> 4 ABCA4 30
+#> 5 ABCB10 5
+#> 6 ABCD3 5
+#> 7 ABL2 8
+#> 8 AC096677.1 3
+#> 9 AC119673.1 1
+#> 10 ACADM 6
+#> 11 ACAP3 7
+#> 12 ACBD3 7
+#> 13 ACBD6 1
+#> 14 ACOT11 8
+#> 15 ACOT7 5
+#> 16 ACP6 4
+#> 17 ACTA1 5
+#> 18 ACTL8 3
+#> 19 ACTN2 15
+#> 20 ACTRT2 1
+#> 21 ADAM15 8
+#> 22 ADAM30 9
+#> 23 ADAMTS4 5
+#> 24 ADAMTSL4 22
+#> 25 ADAMTSL4-AS1 6
+#> Warning: TNFRSF14 could not be fit on page. It will not be plotted.
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+#> Warning: ARHGEF2 could not be fit on page. It will not be plotted.
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+#> Warning: PM20D1 could not be fit on page. It will not be plotted.
+#> Warning: MLLT11 could not be fit on page. It will not be plotted.
+#> Warning: COL24A1 could not be fit on page. It will not be plotted.
+#> Warning: KIAA0907 could not be fit on page. It will not be plotted.
+#> Warning: NPR1 could not be fit on page. It will not be plotted.
+#> Warning: NBPF20 could not be fit on page. It will not be plotted.
+#> Warning: AL590483.1 could not be fit on page. It will not be plotted.
+#> Warning: DHDDS could not be fit on page. It will not be plotted.
+#> Warning: PEX19 could not be fit on page. It will not be plotted.
+#> Warning: ZNF281 could not be fit on page. It will not be plotted.
+#> Warning: HHIPL2 could not be fit on page. It will not be plotted.
+#> Warning: LAPTM5 could not be fit on page. It will not be plotted.
+#> Warning: DDOST could not be fit on page. It will not be plotted.
+#> Warning: COG2 could not be fit on page. It will not be plotted.
+#> Warning: USH2A could not be fit on page. It will not be plotted.
+#> Warning: SPRTN could not be fit on page. It will not be plotted.
+#> Warning: HPDL could not be fit on page. It will not be plotted.
+#> Warning: GPR153 could not be fit on page. It will not be plotted.
+#> Warning: MACF1 could not be fit on page. It will not be plotted.
+#> Warning: GRHL3 could not be fit on page. It will not be plotted.
+#> Warning: SLC44A3 could not be fit on page. It will not be plotted.
+#> Warning: KLHL12 could not be fit on page. It will not be plotted.
+#> Warning: WDR78 could not be fit on page. It will not be plotted.
+#> Warning: GMEB1 could not be fit on page. It will not be plotted.
+#> Warning: MARCKSL1 could not be fit on page. It will not be plotted.
+#> Warning: PTPN14 could not be fit on page. It will not be plotted.
+#> Warning: ZBED6 could not be fit on page. It will not be plotted.
+#> Warning: ABCA4 could not be fit on page. It will not be plotted.
+#> Warning: SELE could not be fit on page. It will not be plotted.
+#> Warning: ZC3H12A could not be fit on page. It will not be plotted.
+#> Warning: SUCO could not be fit on page. It will not be plotted.
+#> Warning: AK5 could not be fit on page. It will not be plotted.
+#> Warning: DEDD could not be fit on page. It will not be plotted.
+#> Warning: FOXD2 could not be fit on page. It will not be plotted.
+#> Warning: EXOC8 could not be fit on page. It will not be plotted.
+#> Warning: OR2L5 could not be fit on page. It will not be plotted.
+#> Warning: ZBTB37 could not be fit on page. It will not be plotted.
+#> Warning: VTCN1 could not be fit on page. It will not be plotted.
+#> Warning: SLAMF1 could not be fit on page. It will not be plotted.
+#> Warning: ANP32E could not be fit on page. It will not be plotted.
+#> Warning: ZRANB2 could not be fit on page. It will not be plotted.
+#> Warning: NPHP4 could not be fit on page. It will not be plotted.
+#> Warning: LYST could not be fit on page. It will not be plotted.
+#> Warning: CTSS could not be fit on page. It will not be plotted.
+#> Warning: POU2F1 could not be fit on page. It will not be plotted.
+#> Warning: FNBP1L could not be fit on page. It will not be plotted.
+#> Warning: ZNF669 could not be fit on page. It will not be plotted.
+#> Warning: PGBD5 could not be fit on page. It will not be plotted.
+#> Warning: CCDC27 could not be fit on page. It will not be plotted.
+#> Warning: C8A could not be fit on page. It will not be plotted.
+#> Warning: PAPPA2 could not be fit on page. It will not be plotted.
+#> Warning: NFYC could not be fit on page. It will not be plotted.
+#> Warning: RPL11 could not be fit on page. It will not be plotted.
+#> Warning: TMCO4 could not be fit on page. It will not be plotted.
+#> Warning: DMBX1 could not be fit on page. It will not be plotted.
+#> Warning: CCSAP could not be fit on page. It will not be plotted.
+#> Warning: PRDM16 could not be fit on page. It will not be plotted.
+#> Warning: C1orf86 could not be fit on page. It will not be plotted.
+#> Warning: SSX2IP could not be fit on page. It will not be plotted.
+#> Warning: KIF26B could not be fit on page. It will not be plotted.
+#> Warning: DOCK7 could not be fit on page. It will not be plotted.
+#> Warning: WDTC1 could not be fit on page. It will not be plotted.
+#> Warning: RRP15 could not be fit on page. It will not be plotted.
+#> Warning: SEMA6C could not be fit on page. It will not be plotted.
+#> Warning: SLFNL1 could not be fit on page. It will not be plotted.
+#> Warning: PVRL4 could not be fit on page. It will not be plotted.
+#> Warning: TMEM56 could not be fit on page. It will not be plotted.
+#> Warning: SMG5 could not be fit on page. It will not be plotted.
+#> Warning: GNAT2 could not be fit on page. It will not be plotted.
+#> Warning: LRRC8D could not be fit on page. It will not be plotted.
+#> Warning: KCNA10 could not be fit on page. It will not be plotted.
+#> Warning: AC096677.1 could not be fit on page. It will not be plotted.
+#> Warning: CR1L could not be fit on page. It will not be plotted.
+#> Warning: APH1A could not be fit on page. It will not be plotted.
+#> Warning: ZSWIM5 could not be fit on page. It will not be plotted.
+#> Warning: CAMTA1 could not be fit on page. It will not be plotted.
+#> Warning: ANGPTL1 could not be fit on page. It will not be plotted.
+#> Warning: ZC3H11A could not be fit on page. It will not be plotted.
+#> Warning: NUDC could not be fit on page. It will not be plotted.
+#> Warning: NAV1 could not be fit on page. It will not be plotted.
+#> Warning: ADIPOR1 could not be fit on page. It will not be plotted.
+#> Warning: WRAP73 could not be fit on page. It will not be plotted.
+#> Warning: CYP4B1 could not be fit on page. It will not be plotted.
+#> Warning: THRAP3 could not be fit on page. It will not be plotted.
+#> Warning: AVPR1B could not be fit on page. It will not be plotted.
+#> Warning: RP11-436K8.1 could not be fit on page. It will not be plotted.
+#> Warning: NMNAT2 could not be fit on page. It will not be plotted.
+#> Warning: MAST2 could not be fit on page. It will not be plotted.
+#> Warning: ITGB3BP could not be fit on page. It will not be plotted.
+#> Warning: CNST could not be fit on page. It will not be plotted.
+#> Warning: CHML could not be fit on page. It will not be plotted.
+#> Warning: ACBD3 could not be fit on page. It will not be plotted.
+#> Warning: EPHA10 could not be fit on page. It will not be plotted.
+#> Warning: NR0B2 could not be fit on page. It will not be plotted.
+#> Warning: HFM1 could not be fit on page. It will not be plotted.
+#> Warning: ELTD1 could not be fit on page. It will not be plotted.
+#> Warning: FCRL1 could not be fit on page. It will not be plotted.
+#> Warning: GLMN could not be fit on page. It will not be plotted.
+#> Warning: PDE4B could not be fit on page. It will not be plotted.
+#> Warning: PIK3R3 could not be fit on page. It will not be plotted.
+#> Warning: ANGPTL3 could not be fit on page. It will not be plotted.
+#> Warning: UBE2J2 could not be fit on page. It will not be plotted.
+#> Warning: C1orf56 could not be fit on page. It will not be plotted.
+#> Warning: BRINP2 could not be fit on page. It will not be plotted.
+#> Warning: BTBD8 could not be fit on page. It will not be plotted.
+#> Warning: TFAP2E could not be fit on page. It will not be plotted.
+#> Warning: IQGAP3 could not be fit on page. It will not be plotted.
+#> Warning: DMRTA2 could not be fit on page. It will not be plotted.
+#> Warning: ZBTB18 could not be fit on page. It will not be plotted.
+#> Warning: STRIP1 could not be fit on page. It will not be plotted.
+#> Warning: TMEM206 could not be fit on page. It will not be plotted.
+#> Warning: RAP1GAP could not be fit on page. It will not be plotted.
+#> Warning: WDR26 could not be fit on page. It will not be plotted.
+#> Warning: TAS1R3 could not be fit on page. It will not be plotted.
+#> Warning: OPN3 could not be fit on page. It will not be plotted.
+#> Warning: SLC19A2 could not be fit on page. It will not be plotted.
+#> Warning: SZT2 could not be fit on page. It will not be plotted.
+#> Warning: TNNI3K could not be fit on page. It will not be plotted.
+#> Warning: AHDC1 could not be fit on page. It will not be plotted.
+#> Warning: RHOC could not be fit on page. It will not be plotted.
+#> Warning: OR2L3 could not be fit on page. It will not be plotted.
+#> Warning: PIP5K1A could not be fit on page. It will not be plotted.
+#> Warning: CDC20 could not be fit on page. It will not be plotted.
+#> Warning: SLC30A10 could not be fit on page. It will not be plotted.
+#> Warning: FMN2 could not be fit on page. It will not be plotted.
+#> Warning: OR14K1 could not be fit on page. It will not be plotted.
+#> Warning: RPL22 could not be fit on page. It will not be plotted.
+#> Warning: SPOCD1 could not be fit on page. It will not be plotted.
+#> Warning: ITGA10 could not be fit on page. It will not be plotted.
+#> Warning: ADAM30 could not be fit on page. It will not be plotted.
+#> Warning: FMO1 could not be fit on page. It will not be plotted.
+#> Warning: ETV3 could not be fit on page. It will not be plotted.
+#> Warning: FAM73A could not be fit on page. It will not be plotted.
+#> Warning: TP73 could not be fit on page. It will not be plotted.
+#> Warning: FCRLA could not be fit on page. It will not be plotted.
+#> Warning: TEX35 could not be fit on page. It will not be plotted.
+#> Warning: RORC could not be fit on page. It will not be plotted.
+#> Warning: EDEM3 could not be fit on page. It will not be plotted.
+#> Warning: OTUD3 could not be fit on page. It will not be plotted.
+#> Warning: ATPAF1 could not be fit on page. It will not be plotted.
+#> Warning: NFASC could not be fit on page. It will not be plotted.
+#> Warning: MARC2 could not be fit on page. It will not be plotted.
+#> Warning: SLC27A3 could not be fit on page. It will not be plotted.
+#> Warning: KCNN3 could not be fit on page. It will not be plotted.
+#> Warning: FAM46C could not be fit on page. It will not be plotted.
+#> Warning: IGFN1 could not be fit on page. It will not be plotted.
+#> Warning: ZNF692 could not be fit on page. It will not be plotted.
+#> Warning: TRABD2B could not be fit on page. It will not be plotted.
+#> Warning: DNTTIP2 could not be fit on page. It will not be plotted.
+#> Warning: HIST2H3D could not be fit on page. It will not be plotted.
+#> Warning: JMJD4 could not be fit on page. It will not be plotted.
+#> Warning: AGBL4 could not be fit on page. It will not be plotted.
+#> Warning: PER3 could not be fit on page. It will not be plotted.
+#> Warning: RUNX3 could not be fit on page. It will not be plotted.
+#> Warning: ACTN2 could not be fit on page. It will not be plotted.
+#> Warning: CSF1 could not be fit on page. It will not be plotted.
+#> Warning: KIAA1614 could not be fit on page. It will not be plotted.
+#> Warning: IFRG15 could not be fit on page. It will not be plotted.
+#> Warning: SCYL3 could not be fit on page. It will not be plotted.
+#> Warning: OR2L8 could not be fit on page. It will not be plotted.
+#> Warning: NTNG1 could not be fit on page. It will not be plotted.
+#> Warning: DIEXF could not be fit on page. It will not be plotted.
+#> Warning: AKR7A2 could not be fit on page. It will not be plotted.
+#> Warning: METTL18 could not be fit on page. It will not be plotted.
+#> Warning: KCTD3 could not be fit on page. It will not be plotted.
+#> Warning: KIF21B could not be fit on page. It will not be plotted.
+#> Warning: NOS1AP could not be fit on page. It will not be plotted.
+#> Warning: YOD1 could not be fit on page. It will not be plotted.
+#> Warning: SH2D1B could not be fit on page. It will not be plotted.
+#> Warning: GBP7 could not be fit on page. It will not be plotted.
+#> Warning: AL109659.1 could not be fit on page. It will not be plotted.
+#> Warning: C1orf63 could not be fit on page. It will not be plotted.
+#> Warning: DAP3 could not be fit on page. It will not be plotted.
+#> Warning: EXTL2 could not be fit on page. It will not be plotted.
+#> Warning: LEPRE1 could not be fit on page. It will not be plotted.
+#> Warning: SIPA1L2 could not be fit on page. It will not be plotted.
+#> Warning: SHCBP1L could not be fit on page. It will not be plotted.
+#> Warning: NCSTN could not be fit on page. It will not be plotted.
+#> Warning: HHLA3 could not be fit on page. It will not be plotted.
+#> Warning: RASAL2 could not be fit on page. It will not be plotted.
+#> Warning: KIF17 could not be fit on page. It will not be plotted.
+#> Warning: FMO5 could not be fit on page. It will not be plotted.
+#> Warning: TRAF3IP3 could not be fit on page. It will not be plotted.
+#> Warning: FBXO42 could not be fit on page. It will not be plotted.
+#> Warning: LYSMD1 could not be fit on page. It will not be plotted.
+#> Warning: H6PD could not be fit on page. It will not be plotted.
+#> Warning: ZNF695 could not be fit on page. It will not be plotted.
+#> Warning: PPM1J could not be fit on page. It will not be plotted.
+#> Warning: PIK3C2B could not be fit on page. It will not be plotted.
+#> Warning: WDR3 could not be fit on page. It will not be plotted.
+#> Warning: MYBPHL could not be fit on page. It will not be plotted.
+#> Warning: CD34 could not be fit on page. It will not be plotted.
+#> Warning: RP11-400N13.3 could not be fit on page. It will not be plotted.
+#> Warning: VCAM1 could not be fit on page. It will not be plotted.
+#> Warning: DDAH1 could not be fit on page. It will not be plotted.
+#> Warning: NUP210L could not be fit on page. It will not be plotted.
+#> Warning: TNR could not be fit on page. It will not be plotted.
+#> Warning: TRAF5 could not be fit on page. It will not be plotted.
+#> Warning: WNT4 could not be fit on page. It will not be plotted.
+#> Warning: KIFAP3 could not be fit on page. It will not be plotted.
+#> Warning: PPP1R12B could not be fit on page. It will not be plotted.
+#> Warning: NRAS could not be fit on page. It will not be plotted.
+#> Warning: MEGF6 could not be fit on page. It will not be plotted.
+#> Warning: DHCR24 could not be fit on page. It will not be plotted.
+#> Warning: GBP6 could not be fit on page. It will not be plotted.
+#> Warning: UHMK1 could not be fit on page. It will not be plotted.
+#> Warning: DCST1 could not be fit on page. It will not be plotted.
+#> Warning: NOC2L could not be fit on page. It will not be plotted.
+#> Warning: COL9A2 could not be fit on page. It will not be plotted.
+#> Warning: KPNA6 could not be fit on page. It will not be plotted.
+#> Warning: OR2AK2 could not be fit on page. It will not be plotted.
+#> Warning: IARS2 could not be fit on page. It will not be plotted.
+#> Warning: C1orf177 could not be fit on page. It will not be plotted.
+#> Warning: CAPZB could not be fit on page. It will not be plotted.
+#> Warning: C1orf185 could not be fit on page. It will not be plotted.
+#> Warning: CHD5 could not be fit on page. It will not be plotted.
+#> Warning: ALDH9A1 could not be fit on page. It will not be plotted.
+#> Warning: HAO2 could not be fit on page. It will not be plotted.
+#> Warning: CYP4Z2P could not be fit on page. It will not be plotted.
+#> Warning: ST6GALNAC3 could not be fit on page. It will not be plotted.
+#> Warning: AMY2B could not be fit on page. It will not be plotted.
+#> Warning: ATP1A2 could not be fit on page. It will not be plotted.
+#> Warning: ZFP69B could not be fit on page. It will not be plotted.
+#> Warning: TGFBR3 could not be fit on page. It will not be plotted.
+#> Warning: TRIM63 could not be fit on page. It will not be plotted.
+#> Warning: CLSTN1 could not be fit on page. It will not be plotted.
+#> Warning: ZNF678 could not be fit on page. It will not be plotted.
+#> Warning: HIST2H2AB could not be fit on page. It will not be plotted.
+#> Warning: LRP8 could not be fit on page. It will not be plotted.
+#> Warning: B3GALNT2 could not be fit on page. It will not be plotted.
+#> Warning: ABCB10 could not be fit on page. It will not be plotted.
+#> Warning: CACNA1E could not be fit on page. It will not be plotted.
+#> Warning: ACADM could not be fit on page. It will not be plotted.
+#> Warning: MAN1C1 could not be fit on page. It will not be plotted.
+#> Warning: AMPD1 could not be fit on page. It will not be plotted.
+#> Warning: RCAN3 could not be fit on page. It will not be plotted.
+#> Warning: LPHN2 could not be fit on page. It will not be plotted.
+#> Warning: RXFP4 could not be fit on page. It will not be plotted.
+#> Warning: CFH could not be fit on page. It will not be plotted.
+#> Warning: ANKRD45 could not be fit on page. It will not be plotted.
+#> Warning: C1orf216 could not be fit on page. It will not be plotted.
+#> Warning: EYA3 could not be fit on page. It will not be plotted.
+#> Warning: S1PR1 could not be fit on page. It will not be plotted.
+#> Warning: KCNJ9 could not be fit on page. It will not be plotted.
+#> Warning: FLG2 could not be fit on page. It will not be plotted.
+#> Warning: YTHDF2 could not be fit on page. It will not be plotted.
+#> Warning: SHC1 could not be fit on page. It will not be plotted.
+#> Warning: SEC16B could not be fit on page. It will not be plotted.
+#> Warning: CYP4Z1 could not be fit on page. It will not be plotted.
+#> Warning: CA14 could not be fit on page. It will not be plotted.
+#> Warning: FHAD1 could not be fit on page. It will not be plotted.
+#> Warning: SLC44A5 could not be fit on page. It will not be plotted.
+#> Warning: OR2T12 could not be fit on page. It will not be plotted.
+#> Warning: C1orf116 could not be fit on page. It will not be plotted.
+#> Warning: AGO3 could not be fit on page. It will not be plotted.
+#> Warning: CLCNKB could not be fit on page. It will not be plotted.
+#> Warning: LRRC53 could not be fit on page. It will not be plotted.
+#> Warning: OR2T11 could not be fit on page. It will not be plotted.
+#> Warning: TMEM61 could not be fit on page. It will not be plotted.
+#> Warning: KIAA1107 could not be fit on page. It will not be plotted.
+#> Warning: CDK18 could not be fit on page. It will not be plotted.
+#> Warning: RPTN could not be fit on page. It will not be plotted.
+#> Warning: RGS16 could not be fit on page. It will not be plotted.
+#> Warning: TOE1 could not be fit on page. It will not be plotted.
+#> Warning: SYCP1 could not be fit on page. It will not be plotted.
+#> Warning: ARHGEF16 could not be fit on page. It will not be plotted.
+#> Warning: CHRNB2 could not be fit on page. It will not be plotted.
+#> Warning: MMACHC could not be fit on page. It will not be plotted.
+#> Warning: ZBTB7B could not be fit on page. It will not be plotted.
+#> Warning: DNASE2B could not be fit on page. It will not be plotted.
+#> Warning: SH2D5 could not be fit on page. It will not be plotted.
+#> Warning: PRRC2C could not be fit on page. It will not be plotted.
+#> Warning: GPATCH3 could not be fit on page. It will not be plotted.
+#> Warning: TGFB2 could not be fit on page. It will not be plotted.
+#> Warning: DUSP12 could not be fit on page. It will not be plotted.
+#> Warning: LMX1A could not be fit on page. It will not be plotted.
+#> Warning: AKNAD1 could not be fit on page. It will not be plotted.
+#> Warning: DNAJC16 could not be fit on page. It will not be plotted.
+#> Warning: WNT9A could not be fit on page. It will not be plotted.
+#> Warning: ADAMTSL4 could not be fit on page. It will not be plotted.
+#> Warning: HOOK1 could not be fit on page. It will not be plotted.
+#> Warning: CASQ1 could not be fit on page. It will not be plotted.
+#> Warning: RTCA could not be fit on page. It will not be plotted.
+#> Warning: PTPN22 could not be fit on page. It will not be plotted.
+#> Warning: BCAR3 could not be fit on page. It will not be plotted.
+#> Warning: EFCAB14 could not be fit on page. It will not be plotted.
+#> Warning: TARS2 could not be fit on page. It will not be plotted.
+#> Warning: CGN could not be fit on page. It will not be plotted.
+#> Warning: KAZN could not be fit on page. It will not be plotted.
+#> Warning: TTC34 could not be fit on page. It will not be plotted.
+#> Warning: HCN3 could not be fit on page. It will not be plotted.
+#> Warning: ST3GAL3 could not be fit on page. It will not be plotted.
+#> Warning: C1orf229 could not be fit on page. It will not be plotted.
+#> Warning: ARHGAP30 could not be fit on page. It will not be plotted.
+#> Warning: PTGS2 could not be fit on page. It will not be plotted.
+#> Warning: EPS8L3 could not be fit on page. It will not be plotted.
+#> Warning: RNF2 could not be fit on page. It will not be plotted.
+#> Warning: C1orf213 could not be fit on page. It will not be plotted.
+#> Warning: SAMD11 could not be fit on page. It will not be plotted.
+#> Warning: CAPN8 could not be fit on page. It will not be plotted.
+#> Warning: SUSD4 could not be fit on page. It will not be plotted.
+#> Warning: FMO2 could not be fit on page. It will not be plotted.
+#> Warning: HSPA6 could not be fit on page. It will not be plotted.
+#> Warning: ATP2B4 could not be fit on page. It will not be plotted.
+#> Warning: CTTNBP2NL could not be fit on page. It will not be plotted.
+#> Warning: OLFML2B could not be fit on page. It will not be plotted.
+#> Warning: PLD5 could not be fit on page. It will not be plotted.
+#> Warning: ATP8B2 could not be fit on page. It will not be plotted.
+#> Warning: MLK4 could not be fit on page. It will not be plotted.
+#> Warning: CFHR4 could not be fit on page. It will not be plotted.
+#> Warning: OAZ3 could not be fit on page. It will not be plotted.
+#> Warning: CASZ1 could not be fit on page. It will not be plotted.
+#> Warning: DHRS3 could not be fit on page. It will not be plotted.
+#> Warning: NBPF9 could not be fit on page. It will not be plotted.
+#> Warning: OR2L13 could not be fit on page. It will not be plotted.
+#> Warning: ECM1 could not be fit on page. It will not be plotted.
+#> Warning: FMOD could not be fit on page. It will not be plotted.
+#> Warning: PADI1 could not be fit on page. It will not be plotted.
+#> Warning: TNFSF18 could not be fit on page. It will not be plotted.
+#> Warning: NDUFS2 could not be fit on page. It will not be plotted.
+#> Warning: PGLYRP4 could not be fit on page. It will not be plotted.
+#> Warning: TYW3 could not be fit on page. It will not be plotted.
+#> Warning: ZNF691 could not be fit on page. It will not be plotted.
+#> Warning: TIE1 could not be fit on page. It will not be plotted.
+#> Warning: TMEM63A could not be fit on page. It will not be plotted.
+#> Warning: GUCA2B could not be fit on page. It will not be plotted.
+
+#> # A tibble: 2,006 × 2
+#> Hugo_Symbol n
+#> <fct> <int>
+#> 1 AC119673.1 1
+#> 2 ACBD6 1
+#> 3 ACTRT2 1
+#> 4 AGTRAP 1
+#> 5 AHCYL1 1
+#> 6 AKIRIN1 1
+#> 7 AL109927.1 1
+#> 8 AL136115.1 1
+#> 9 AL138847.1 1
+#> 10 AL139147.1 1
+#> # ℹ 1,996 more rows
#multi-sample rainfall plot for one gene region
prettyRainfallPlot(zoom_in_region = "chr3:5,221,286-5,269,723",
@@ -181,8 +212,7 @@ 
diff --git a/docs/reference/pretty_lollipop_plot.html b/docs/reference/pretty_lollipop_plot.html
index 3087bad3..5a913324 100644
--- a/docs/reference/pretty_lollipop_plot.html
+++ b/docs/reference/pretty_lollipop_plot.html
@@ -8,7 +8,7 @@
gtag('js', new Date());
gtag('config', 'UA-12345678-0');
-
+
pretty_lollipop_plot(maf_df, gene, plot_title, plot_theme = "cbioportal")pretty_lollipop_plot(
+ maf_df,
+ gene,
+ plot_title,
+ plot_theme = "cbioportal",
+ out_name = paste0("my_lollipop_plot_", gene)
+)Options: cbioportal(default), blue, simple, nature, nature2, ggplot2, and dark.
Optional, set the file name of the plot, if you export it to disk. Default name is my_lollipop_plot_gene.
#get metadata (Fl and DLBCL)
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
this_metadata = dplyr::filter(metadata, consensus_pathology %in% c("FL", "DLBCL"))
-#> Error in dplyr::filter(metadata, consensus_pathology %in% c("FL", "DLBCL")): object 'metadata' not found
#get maf data for returned samples
maf = get_coding_ssm(limit_samples = this_metadata$sample_id,
seq_type = "genome")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 826 samples
#construct pretty_lollipop_plot.
pretty_lollipop_plot(maf_df = maf,
gene = "MYC",
plot_title = "Mutation data for MYC",
plot_theme = "nature2")
-#> Error in dplyr::filter(., Hugo_Symbol == gene): object 'maf' not found
-
+#> Factor is set to Mutation_Class
+#> legend title is set to Mutation_Class
+
+
process_all_manta_bedpe.RdThis function is in draft mode.
-process_all_manta_bedpe(
- file_df,
- out_dir,
- group,
- genome_build,
- projection_build = "grch37"
-)Paths to bedpe.
output directory.
The unix group.
Genome build.
The genome we want all results to be relative to (lifted if necessary).
This is a helper function that is not meant to be used routinely.
-read_merge_manta_with_liftover.RdTakes a path to bedpe and runs liftover (liftover_bedpe) based on the original genome build of the bedpe.
-read_merge_manta_with_liftover(
- bedpe_paths = c(),
- pattern = "--matched",
- out_dir
-)path to bedpe
pattern
output directory
This is a helper function that is not meant to be used routinely.
-if (FALSE) {
-manta_bedpe = read_merge_manta_with_liftover(bedpe_paths = "some_path.bedpe",
- out_dir = "../")
-}
-
-referesh_metadata_tables.RdRefresh the contents of a metadata table.
-referesh_metadata_tables()Table.
-INTERNAL FUNCTION, not meant for out-of-package usage.
-if (FALSE) {
-ref_meta = referesh_metadata_tables()
-}
-
-refresh_full_table.RdRefresh the contents of a database table.
-refresh_full_table(table_name, connection, file_path)Name of table to refresh.
Database connection object.
Path to the table contents to populate.
A table.
-INTERNAL FUNCTION called by referesh_metadata_tables, not meant for out-of-package usage.
-if (FALSE) {
-refresh_full_table(table_x, con,file_x)
-}
-
-region_to_chunks.RdParse a region string into; chromosome, start and end.
-region_to_chunks(region)A region string e.g. "chrX:12345-678910".
A named list.
-INTERNAL FUNCTION called by calc_mutation_frequency_sliding_windows, not meant for out-of-package usage.
-if (FALSE) {
-chr_start_end = region_to_chunks("chr1:1111-2222")
-}
-
-hot_ssms = review_hotspots(annotate_hotspots(get_coding_ssm(seq_type = "genome")),
genes_of_interest = c("CREBBP"))
-#> Error: '/Users/rmorin/git/gambl/versioned_results/oncodriveclustl-0.0_FL--DLBCL_clusters_results.tsv' does not exist.
+#> Adding missing grouping variables: `SYMBOL`
+#> Adding missing grouping variables: `SYMBOL`
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/genome--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 1652 samples
+#> after linking with metadata, we have mutations from 1646 samples
diff --git a/docs/reference/sanity_check_metadata.html b/docs/reference/sanity_check_metadata.html
deleted file mode 100644
index d4785458..00000000
--- a/docs/reference/sanity_check_metadata.html
+++ /dev/null
@@ -1,111 +0,0 @@
-
-sanity_check_metadata.RdFunction that performs sanity checks on metadata.
-sanity_check_metadata()A table.
-Helper function for sanity checking GAMBL metadata.
-if (FALSE) {
-sane_meta_data = sanity_check_metadata()
-}
-
-standardize_chr_prefix.RdStandardize the chr prefix in a vector of chromosome names based on projection.
-standardize_chr_prefix(incoming_vector, projection)Input vector of any length with chromosome names.
Projection to which chr prefix should be standardized.
A vector of chromosome names with prefix standardized to projection
-INTERNAL FUNCTION, not meant for out-of-package use.
-these_chrs = c(8, "13", "chr4", "chrY")
-
-standardize_chr_prefix(incoming_vector = these_chrs,
- projection = "hg38")
-#> Error in standardize_chr_prefix(incoming_vector = these_chrs, projection = "hg38"): could not find function "standardize_chr_prefix"
-
-subset_cnstates.RdGet the available CN states in the incoming data frame.
-subset_cnstates(cn_segments, include_2 = FALSE, samplen)DF with copy number segments, usually retrieved from get_sample_cn_segments.
Optional parameter for including or omit CN state == 2. Default is FALSE.
Numeric value that annotates the sample order.
Nothing.
-INTERNAL FUNCTION called by fancy_multisample_ideo, for sub-setting copy number information based on segments available in cn data
-cn_states = get_sample_cn_segments(multiple_samples = TRUE,
- sample_list = c("00-15201_tumorA",
- "HTMCP-01-06-00422-01A-01D"),
- streamlined = FALSE)
-
-subset_cnstates(cn_segments = cn_states,
- samplen = 1)
-#> Error in subset_cnstates(cn_segments = cn_states, samplen = 1): could not find function "subset_cnstates"
-
-small_maf = get_coding_ssm(limit_cohort = "dlbcl_reddy",
seq_type = "capture")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
+#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
+#> mutations from 2343 samples
+#> after linking with metadata, we have mutations from 989 samples
small_maf = dplyr::filter(small_maf, Hugo_Symbol == "MYC")
-#> Error in dplyr::filter(small_maf, Hugo_Symbol == "MYC"): object 'small_maf' not found
my_metadata = get_gambl_metadata(seq_type_filter = "capture")
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
reddy_meta = dplyr::filter(my_metadata, cohort=="dlbcl_reddy")
-#> Error in dplyr::filter(my_metadata, cohort == "dlbcl_reddy"): object 'my_metadata' not found
complete_maf = supplement_maf(incoming_maf = small_maf,
these_samples_metadata = reddy_meta)
-#> Error in setdiff(these_samples_metadata$Tumor_Sample_Barcode, incoming_maf$Tumor_Sample_Barcode): object 'reddy_meta' not found
metadata = get_gambl_metadata()
-#> [1] "missing: /Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv"
-#> Have you cloned the GAMBL repo and added the path to this directory under the local section of your config?
-#> Error: '/Users/rmorin/git/gambl/data/metadata/gambl_all_outcomes.tsv' does not exist.
lymphgen = tidy_lymphgen(df = metadata,
lymphgen_column_in = "lymphgen_with_cnv",
lymphgen_column_out = "lymphgen_with_cnv_tidy",
relevel = TRUE)
-#> Error in mutate(df, `:=`({ { lymphgen_column_out }}, case_when(!str_detect(.data[[lymphgen_column_in]], "/") ~ .data[[lymphgen_column_in]], str_detect(.data[[lymphgen_column_in]], "EZB") ~ "EZB-COMP", str_detect(.data[[lymphgen_column_in]], "MCD") ~ "MCD-COMP", str_detect(.data[[lymphgen_column_in]], "N1") ~ "N1-COMP", str_detect(.data[[lymphgen_column_in]], "BN2") ~ "BN2-COMP", str_detect(.data[[lymphgen_column_in]], "ST2") ~ "ST2-COMP"))): object 'metadata' not found
trim_scale_expression.RdINTERNAL FUNCTION called by prettyOncoplot, not meant for out-of-package usage.
-trim_scale_expression(x)Numeric value (of expression) to be trimmed.
Numeric value.
-INTERNAL FUNCTION called by prettyOncoplot, not meant for out-of-package usage.
-if (FALSE) {
-trimmed = trim_scale_expression(2)
-}
-
-web_initialize_gambl_site.RdSet up a fresh instance of a website to host on gitlab.
-web_initialize_gambl_site(
- site_base_name,
- base_directory = "/home/rmorin/",
- my_name = "Ryan Morin",
- my_gitlab_email = "rdmorin@sfu.ca"
-)Base name for site.
Path to base directory.
My name.
The email used for gitlab.