RATs v0.6.0 (R source package)

Changes in v0.6.0

• Support for input directly from sleuth objects has been removed. ( #33 ) This is due to changes in sleuth 0.29 that result in the bootstrap data no longer been available. An alternative has already been in place via fish4rodents() which allows input of bootstrap data directly from the Kallisto/Salmon quantifications.
• The rrep_as_crit parameter has been removed. the same effect can be achieved more transparently by setting rrep_thresh to 0.

Bugfixes

• An off-by-one error in the reporting functions for isoform switch events has been fixed. ( #34 )
• Out of date function docs have been fixed.

Changes in v0.5.0

Despite drafting the release of 0.5.0, I realised too late that I never actually packaged up and published it. Several important changes were made in it and they still apply to 0.6.0, so I'm including them here.

New features

1. The $Transcripts table records absolute fold-change per transcript (log2FC). How meaningful that is will depend on whether your input abundances are normalised across replicates or not. RATs currently does not normalise across replicates (except for data imported via fish4rodents(), see below), because proportions are by definition already normalised for size.
2. A new overview plot maps the fold-change against the difference in proportion ("fcVSdprop"). Same caveat as above.
3. Directly import from Salmon/Kallisto output using fish4rodents(). This saves a little time and a lot of memory, compared to importing via Sleuth.
4. The volcano plot can now also be done for genes, instead of only for transcripts.
5. In overview plots, DTU-positive points are always layered over the DTU-negative points, ensuring none are hidden.
6. The histogram of effect sizes can now be made for both transcripts and genes.
7. A scaling factor for abundances is introduced. This could be useful when running RATs with TPM or similar normalised abundances, as 1 million transcripts is a gross under-estimation of the library size. Scaling the TPM accordingly would improve statistical power of RATS. Misuse of scaling will artificially inflate or deflate the significance of the observed differences!

Other improvements

1. Styling tweaks to gene and overview plots to reduce clutter and improve encoding consistency.
2. The summary reports are now presented as data.frames instead of named vectors. This makes them much more legible.
3. The replicate lines in the gene plot are now slightly offset, to avoid becoming hidden by one another when the measurements are very similar.
4. The interactive volcano plot now plots genes instead of transcripts. Hovering will provide brief info on the gene(s) under(/near) the pointer, clicking will pull up all the relevant information from the $Genes and $Transcripts tables for that gene and produce the relevant gene plot.
5. The histogram of gene effect sizes now segregates positive and negative changes rather than showing the absolute values.
6. General documentation improvements.
7. Un-complicate parts of the code.
8. Bootstrapping the replicates previously used a single sample from each condition "as is". This was not relatable to comparing one set of replicates against another and generally was extremely conservative and unhelpful. In this version, this alleviated by scaling the chosen samples by the number of samples per condition.

Bugfixes

1. Restored table of contents for the vignettes.
2. In the summaries, NA genes for transcript-level and both-levels tallies are now reported correctly instead of being always 0.
3. Fixed some hard-coded field names that could cause failure with non-standard input field names.
4. Better protection against entries in the annotation and abundances being in incompatible orders.

Other changes

1. Optional dependency added for wasabi. Needed when importing data from Salmon.
2. Plot improvements require ggplot2 version >= 2.2.0.
3. The use of multi-threading by-default by data.table, means that RATs now requires version >= 1.9.8 in order to prevent mismanagement of resources.