Initial release. Some of the functions defined in this package have been migrated from my bcbioRNASeq R package.
contrastSamples: Experimental. Return the samples used to generate a corresponding
DESeqResultsobject. May revise this approach to simply store the sample names directly in the
DESeqResultsin the future.
deg: Utility function to obtain DEG gene vector.
resultsTables: Migrated from bcbioRNASeq. Enables easy output of directional DEG tables from
.matchResultsinternal utility to match
plotDEGPCA. May add this back in a future release to maintain compatibility with bcbioRNASeq workflow paper.
DESeqAnalysisS4 data set (
updateObject, which must be added in future update.
results = 1Lby default in
DESeqAnalysismethods for functions that support pulling a
DESeqResultsobject. This can result in unwanted behavior, and we shouldn’t assume use of first slotted contrast. Now the user must request the desired contrast explicitly.
resultsTablesgenerics (verbs) to bioverbs.
validateS4code, instead relying upon
nullOK = TRUE, where applicable. This was added in the corresponding release update to goalie.
containsAlphafor assert check.
DESeqAnalysis-classand the corresponding generator function. Refer to the roxygen syntax (e.g.
rdname) on how to accomplish this, since it is useful across packages that define S4 class.
This release reworks the S4 class structure and adds
DESeqAnalysisList. Note that objects previously saved prior to the v0.1.8 release will no longer return valid when checked using
validObject. They can be updated using
SimpleList, and enables saving of multiple analyses (e.g. per patient clinical data) in a single object. This class makes it much easier to report on multiple complex contrasts.
DESeqAnalysisnow inherits from
Annotatedclass. This enables support for
metadataslot, which can be used to store package version.
plotCountsgeneric, in favor of now deprecated
lfcShrinktype (e.g. apeglm).
sampleDatamethod support for
DESeqAnalysis, thereby simplying the
sample_datachunk in differential expression R Markdown template.
DESeqAnalysis. This now will return the version of DESeqAnalysis and not just DESeq2.
plotDEGPCA: Reworked internal code to export
DESeqResultsmethod that maintains backward compatibility with approach used in bcbioRNASeq F1000 paper.
DESeqResultsmethod support for
topTables, to maintain backward compatibility with bcbioRNASeq R package.
DESeqDataSetmethod support, which is now covered inside
SummarizedExperimentmethod support in basejump.
acidprefix instead of
resultsMatrix: Utility function that quickly aggregates
DESeqResultsvalues for multiple contrasts into a single
matrix. Currently supports return of
plotVolcano: Improved color support and gene-to-symbol handling.
Bug fixes to improve handling of
DESeqDataSet generated using RefSeq gene annotations.
contrastNames: Improved internal regular expression matching to properly detect a contrast factor prefix that contains an underscore. This now works by checking against the column names of
geneBiotypeare now optional columns.
transformType, which were previously used internally but are generally useful.
plotDEGHeatmap: Improved default color breaks. Now defaults to blue-black-yellow default color scheme (see
.matchResultsfunction in favor of consistently using
resultsinstead throughout the package.
lfcShrinkinto object is now optional again.
lfcShrinkargument support to
plotVolcano: Now suppressing duplicate gene message returned by internal
Gene2Symbolcall, which isn’t informative here.
lfcShrinkinformation on plots, where applicable.
plotDEGUpset: Support for easily plotting bidirectional (up/down) DEG intersections across contrasts, using the UpSetR package.
plotPCA: Added improved method support for
DESeqTransform, masking the method exported in DESeq2. Also added corresponding method support for
DESeqAnalysisclass, which uses