- The default "zero-centering" logic is updated in mgheatmap2 when
col
isn't specified, butrecenter
is (backported to release 3.14)
calculateIndividualLogFC
is updated to handle situations when$genes
data.frame has column names that collide with statistics generated from differential expression, likepval
,padg
, andAveExpr
. Thanks to @sandersen12 for the bug report.
- Released to Bioconductor
- Adds support for use of BiocSet as a means by which users can bring their genesets to -- or take them from -- sparrow.
- Improvements to the corplot() functionality contributed by by Arkadiusz Gladki (@gladki). Users can specify the size of the text reported in the bottom half of the pair plot, and spurious/annoying warnings that were produced after a a totally valid call are no longer produced.
- First two parameters in ora() function have been swapped so that the
first parameter (
x
) is the object (data.frame) to run an over representation analysis against, and the second parameter is the GeneSetDb. - scoreSingleSamples no longer drops features in
y
that are not found in the GeneSetDb used for scoring. This was changed so that gsva and ssGSEA scores match the scores produced by a normal GSVA::gsva call. You can set thedrop.unconformed = TRUE
to retain the older behavior.