Version 0.4

DESeqAnalysis 0.4.0 (2021-03-15)

New classes:

• DESeqResultsList: New class and corresponding generator function that enables quick looping operations across related DESeqResults objects. This can be useful instead of DESeqAnalysisList approach for cases where we don’t have all of the original DESeqDataSet objects used to generate the corresponding DESeqResults, which can happen with commercial sequencing vendors and analysis platforms.

Major changes:

• Reworked and improved manual limit handling for plotMA and plotVolcano. By default, this behavior is unchanged from previous release, but now limit overrides can be defined similar to the approach in DESeq2 that uses geneplotter engine internally.

Minor changes:

• Improved information in subtitles for MA, volcano, and other DEG plots.
• alphaThreshold and lfcThreshold return sensible defaults for minimal DESeqResults objects created by coercion of a DataFrame directly.

DESeqAnalysis 0.4.1 (2021-06-29)

Minor changes:

• Needed to update internal calls to guide function defined in ggplot2, which has deprecated use of logical FALSE in favor of "none".

DESeqAnalysis 0.4.2 (2021-07-20)

Minor changes:

• Improved R Markdown template for differential expression report, and added code coverage for rmarkdown::render call in unit tests.

DESeqAnalysis 0.4.3 (2021-07-27)

Minor changes:

• plotVolcano: Bug fix for plot labels not mapping correctly. Expecting “lfcCol”, “negLogAlphaCol” internally, but these were incorrectly mapped to the values expected for plotMA instead. Thanks to @kokyriakidis for noticing this.

DESeqAnalysis 0.4.4 (2021-08-02)

Minor changes:

• apeglmResults: Relaxed assert check on P values when applying adaptive shrinkage via apeglm model.