DESeqDataSetmethod support, which is now covered inside
SummarizedExperimentmethod support in basejump.
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.
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.
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.
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.
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.
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.
Initial release. Some of the functions defined in this package have been migrated from my bcbioRNASeq R package.