diff --git a/R/cool_overlaps.R b/R/cool_overlaps.R index f9d86bf..0b702de 100644 --- a/R/cool_overlaps.R +++ b/R/cool_overlaps.R @@ -113,11 +113,13 @@ cool_overlaps <- function( # When the same columns are provided they will become .x and .y if(start1 == start2) { + original_start1 <- start1 start1 <- paste0(start1, ".x") start2 <- paste0(start2, ".y") } if(end1 == end2) { + original_end1 <- end1 end1 <- paste0(end1, ".x") end2 <- paste0(end2, ".y") @@ -193,6 +195,20 @@ cool_overlaps <- function( overlap ) ) + if(original_start1 %in% colnames(no_annotation)){ + colnames(no_annotation) = gsub( + original_start1, + start1, + colnames(no_annotation) + ) + } + if(original_end1 %in% colnames(no_annotation)){ + colnames(no_annotation) = gsub( + original_end1, + end1, + colnames(no_annotation) + ) + } overlap <- bind_rows( overlap, no_annotation diff --git a/R/data.R b/R/data.R index 70148d2..15f3daa 100644 --- a/R/data.R +++ b/R/data.R @@ -980,3 +980,33 @@ #' \item{Description}{NA.} #' } "protein_domains" + +#' Cytobands coordinates (grch37) +#' +#' A data frame in bed format with coordinates of cytobands relative to grch37. +#' +#' @format ## `cytobands_grch37` +#' A data frame with 862 rows and 5 columns +#' \describe{ +#' \item{cb.chromosome}{Chromosome of the cytoband.} +#' \item{cb.start}{Start position of the cytoband.} +#' \item{cb.end}{End position of the cytoband.} +#' \item{cb.name}{Cytoband name.} +#' \item{label}{Cytoband label.} +#' } +"cytobands_grch37" + +#' Cytobands coordinates (hg38) +#' +#' A data frame in bed format with coordinates of cytobands relative to hg38. +#' +#' @format ## `cytobands_hg38` +#' A data frame with 862 rows and 5 columns +#' \describe{ +#' \item{cb.chromosome}{Chromosome of the cytoband.} +#' \item{cb.start}{Start position of the cytoband.} +#' \item{cb.end}{End position of the cytoband.} +#' \item{cb.name}{Cytoband name.} +#' \item{label}{Cytoband label.} +#' } +"cytobands_hg38" diff --git a/data-raw/DATASET.R b/data-raw/DATASET.R index 5a5cdd9..cc2f3ee 100644 --- a/data-raw/DATASET.R +++ b/data-raw/DATASET.R @@ -509,3 +509,20 @@ protein_domains <- system.file( ) %>% read_tsv() usethis::use_data(protein_domains, overwrite = TRUE) + +# Cytobands +cytobands_grch37 <- system.file( + "extdata", + "cytobands_grch37.tsv", + package = "GAMBLR.data" + ) %>% + read_tsv() +usethis::use_data(cytobands_grch37, overwrite = TRUE) + +cytobands_hg38 <- system.file( + "extdata", + "cytobands_hg38.tsv", + package = "GAMBLR.data" + ) %>% + read_tsv() +usethis::use_data(cytobands_hg38, overwrite = TRUE) diff --git a/data/cytobands_grch37.rda b/data/cytobands_grch37.rda new file mode 100644 index 0000000..e5ac5b4 Binary files /dev/null and b/data/cytobands_grch37.rda differ diff --git a/data/cytobands_hg38.rda b/data/cytobands_hg38.rda new file mode 100644 index 0000000..4366cca Binary files /dev/null and b/data/cytobands_hg38.rda differ diff --git a/inst/extdata/cytobands_grch37.tsv b/inst/extdata/cytobands_grch37.tsv new file mode 100644 index 0000000..7868ef1 --- /dev/null +++ b/inst/extdata/cytobands_grch37.tsv @@ -0,0 +1,863 @@ +cb.chromosome cb.start cb.end cb.name label +1 0 2300000 p36.33 gneg +1 2300000 5400000 p36.32 gpos25 +1 5400000 7200000 p36.31 gneg +1 7200000 9200000 p36.23 gpos25 +1 9200000 12700000 p36.22 gneg +1 12700000 16200000 p36.21 gpos50 +1 16200000 20400000 p36.13 gneg +1 20400000 23900000 p36.12 gpos25 +1 23900000 28000000 p36.11 gneg +1 28000000 30200000 p35.3 gpos25 +1 30200000 32400000 p35.2 gneg +1 32400000 34600000 p35.1 gpos25 +1 34600000 40100000 p34.3 gneg +1 40100000 44100000 p34.2 gpos25 +1 44100000 46800000 p34.1 gneg +1 46800000 50700000 p33 gpos75 +1 50700000 56100000 p32.3 gneg +1 56100000 59000000 p32.2 gpos50 +1 59000000 61300000 p32.1 gneg +1 61300000 68900000 p31.3 gpos50 +1 68900000 69700000 p31.2 gneg +1 69700000 84900000 p31.1 gpos100 +1 84900000 88400000 p22.3 gneg +1 88400000 92000000 p22.2 gpos75 +1 92000000 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63800000 65400000 q11.2 gneg +chrX 65400000 68500000 q12 gpos50 +chrX 68500000 73000000 q13.1 gneg +chrX 73000000 74700000 q13.2 gpos50 +chrX 74700000 76800000 q13.3 gneg +chrX 76800000 85400000 q21.1 gpos100 +chrX 85400000 87000000 q21.2 gneg +chrX 87000000 92700000 q21.31 gpos100 +chrX 92700000 94300000 q21.32 gneg +chrX 94300000 99100000 q21.33 gpos75 +chrX 99100000 103300000 q22.1 gneg +chrX 103300000 104500000 q22.2 gpos50 +chrX 104500000 109400000 q22.3 gneg +chrX 109400000 117400000 q23 gpos75 +chrX 117400000 121800000 q24 gneg +chrX 121800000 129500000 q25 gpos100 +chrX 129500000 131300000 q26.1 gneg +chrX 131300000 134500000 q26.2 gpos25 +chrX 134500000 138900000 q26.3 gneg +chrX 138900000 141200000 q27.1 gpos75 +chrX 141200000 143000000 q27.2 gneg +chrX 143000000 148000000 q27.3 gpos100 +chrX 148000000 156040895 q28 gneg +chrY 0 300000 p11.32 gneg +chrY 300000 600000 p11.31 gpos50 +chrY 600000 10300000 p11.2 gneg +chrY 10300000 10400000 p11.1 acen +chrY 10400000 10600000 q11.1 acen +chrY 10600000 12400000 q11.21 gneg +chrY 12400000 17100000 q11.221 gpos50 +chrY 17100000 19600000 q11.222 gneg +chrY 19600000 23800000 q11.223 gpos50 +chrY 23800000 26600000 q11.23 gneg +chrY 26600000 57227415 q12 gvar diff --git a/man/cytobands_grch37.Rd b/man/cytobands_grch37.Rd new file mode 100644 index 0000000..83dd684 --- /dev/null +++ b/man/cytobands_grch37.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{cytobands_grch37} +\alias{cytobands_grch37} +\title{Cytobands coordinates (grch37)} +\format{ +\subsection{\code{cytobands_grch37}}{ + +A data frame with 862 rows and 5 columns +\describe{ +\item{cb.chromosome}{Chromosome of the cytoband.} +\item{cb.start}{Start position of the cytoband.} +\item{cb.end}{End position of the cytoband.} +\item{cb.name}{Cytoband name.} +\item{label}{Cytoband label.} +} +} +} +\usage{ +cytobands_grch37 +} +\description{ +A data frame in bed format with coordinates of cytobands relative to grch37. +} +\keyword{datasets} diff --git a/man/cytobands_hg38.Rd b/man/cytobands_hg38.Rd new file mode 100644 index 0000000..0607a39 --- /dev/null +++ b/man/cytobands_hg38.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{cytobands_hg38} +\alias{cytobands_hg38} +\title{Cytobands coordinates (hg38)} +\format{ +\subsection{\code{cytobands_hg38}}{ + +A data frame with 862 rows and 5 columns +\describe{ +\item{cb.chromosome}{Chromosome of the cytoband.} +\item{cb.start}{Start position of the cytoband.} +\item{cb.end}{End position of the cytoband.} +\item{cb.name}{Cytoband name.} +\item{label}{Cytoband label.} +} +} +} +\usage{ +cytobands_hg38 +} +\description{ +A data frame in bed format with coordinates of cytobands relative to hg38. +} +\keyword{datasets}