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.