RATs v0.4.0

Changes in v0.4.0

Potentially breaking

1. As a result of added input parameters, the names of some existing parameters have been changed to be clearer:
   count_thresh is now called abund_thresh.
   boots (string) is replaced by qboot (logical).
   bootnum is now called qbootnum.
   conf_thresh is now called qrep_thresh.
2. As a result of added output fields, the names of many existing fields in Genes and Transcripts have been changed to be clearer:
   All boot_* pre-fixed fields are now prefixed with quant_* instead.
   *_conf_* has been renamed to *_reprod_* to emphasise that it refers specifically to reproducibility.
   *_na has been renamed to *_na_freq to emphasise it is a frequency.
3. The order of output fields in Genes and Transcripts has been changed to bring all decision-related flags together near the IDs for easy overview.
4. Parameter fields have also been re-ordered. Additionally the following fields have been renamed:
   count_thresh is now abund_thresh.
   conf_thresh is now quant_reprod_thresh.
   bootstrap (string) is replaced by quant_boot (logical).
   bootnum is now quant_bootnum.
5. CountData is now called Abundances.

New features

New bootstrapping mode:
RATs can now assess inter-sample variability by doing all the available 1vs1 DTU comparisons between the two conditions. A threshold can be set for this reproducibility, that is separate from the threshold used for the pre-existing quantification bootstraps.

• This feature is controlled by three parameters: rboot, rrep_thresh and rrep_as_crit.
• New fields in Parameters, Genes and Transcripts prefixed with rep_*.

Bug fixes

1. RATs now explicitly controls the number of threads used by newer versions of data.table. The default of data.table is to use as many threads as the system allows, which can be different to what a user specified to RATs. Previously, even in single-threaded RATs mode, some data.table operations could be performed multi-threaded.

Documentation

1. Oversized tutorial vignette was split further into smaller more focused and more manageable ones. Three vignettes are now available: Quick Start/Introduction, Input & Settings, Output & Plots.
2. Documentation updated to include the new features.
3. Tweaked package dependency designations.

RATs v0.3.8 - R Source Package

Bugfixes

• The sample_to_covariates table of an input sleuth object is no longer assumed to be a data.frame. Now data.table is also supported. #13

Improvements

• Multi-threading enabled. #12
• Plot colour theme tweaked for better contrast (lighter background).

Rats source package v0.3.6

Changes in 0.3.6 compared to 0.3.4

This version contains mainly documentation improvements at the user level and code maintenance improvements at the developer level.

• Improved wording in docs.
• Added explanatory diagrams in vignette and readme, updated existing ones.
• Switched from large single vignette to multiple smaller ones. Currently 2 vignettes available: (1) Intro/Quick-start and (2) Tutorial.
• R version in $Parameters will be recorded more compactly: only R.Version()["platform"] and R.Version()["version.string"] will be recorded, instead of the full output of R.Version() which contains a lot of redundancy.
• The bootnum parameter is checked more extensively for sensible values. Warnings will be shown to raise awareness of potentially unjustified choices. Execution will not be halted except for serious mismatch between request and data.
• In connection with the above, default bootnum changed from 100 to 0, to force users to consciously choose an appropriate value.
• Some additional unit-tests.
• Fixed printout issue of a missing newline between the progress bar and the following status message.

RATS Source Package v0.3.4

Enhancements

• Gene plot style is now a parameter. Brings back some older styles of the plot.
• Aesthetic optimisation of plots.

Announcement

From now on, version numbers will be staggered, for clarity.

• Odd-number-ending versions (1,3,5,7,9) will be used on developmental versions. The most current version of the repository should always be considered a developmental version and should not be used for reproducible analysis of critical data.
• Even-number-ending versions (0,2,4,6,8) will be used for snapshot releases. For reproducible analysis you must always use the latest packaged release.

Rats source package v0.3.2

Bug fixes

• Distribution plot of max changes in proportion now colours DTU the same way as the volcano plot.
• Fixed minor issue with aggregation of transcript-level DTU for the Gene table's transc_DTU field. It affected genes where the transcript DTUs were a mixture of FALSE and NA only. This did not affect the actual DTU results, but the erroneous value could be confusing to interpret.
• Pre-emptively modified other code locations where NA values could potentially cause unexpected behaviour, despite not having evidence of this actually occurring.

Rats source package v0.3.1

Bugfixes

• Fixed issue where a few fully eligible and fully processed transcripts were improperly getting NA as their final result.

Enhancements

• Gene plot now colours individual points by sample.
• Gene plot now incorporates DTU status of each transcript.

Rats source package v0.3.0

Changes

1. Count data per transcript per replicate per condition now stored in the output DTU object to enable more informative plots.
2. Added a shiny app to allow interactive exploration of volcano plots.
3. Re-vamped plot_gene(). Instead of having to choose between proportions and counts, now both are always displayed. The barplots were replaced with more appropriate boxplots. The individual values from each replicate are also overlayed.

Rats source package v0.2.1

Changes:

1. Tweaked how log-scaling is applied to plots. Scaling the axes was causing errors due to infinity values. Now the values are scaled instead, allowing for finite axes. ggplot2 retains infinity values and displays them on the edge of the plot.
2. Updated the static plot images in vignette, to reflect the above change.

Rats source package v0.2.0

Changes and new features from v0.1.0 to v0.2.0

1. Added the ability to extract transcript and gene IDs for the annotation table directly from a .GTF file.
2. Confidence threshold introduced. This allows the confidence derived from the bootstraps to be used as an additional criterion in calling DTU.
3. conf boolean flag introduced to the results tables, indicating whether the DTU call for the entry passes the confidence threshold.
4. The names of the bootstrap-related columns in the results tables have been slightly modified to be less cryptic.

RATs source package v0.1.0

v0.1.0 - Initial Public Release of RATs.

rats is an R package with which to call Differential Transcript Usage from RNA-seq transcript abundance estimates.

Features

1. Supports data input as either a Sleuth object or generic tables.
2. DTU called at both the transcript level and gene level.
3. Bootstrapped abundance estimates leveraged to provide confidence level in DTU calls.
4. Basic summary and plotting functionality built-in for convenience.
5. Fast and efficient R code. On a good laptop: 20 secs without bootstrapping, +15secs per bootstrap iteration.
6. Written exclusively in R language and distributed as a source package. Compatible with all platforms that have an R engine and meet the package dependencies.
7. Extensive usage tutorial.