Changelog

Source: NEWS.md

sparrow 1.14

Enhancements

  • Updated to support refactored msigdbr package (version >= 10.0.0), which now only includse the human Hallmark genesets internally. The msigdbr package relies on an external (non CRAN) msigdbdf package, for the rest of the (now more recent) definitions of the MSigDB gene set collections.

Enhancements

  • The default “zero-centering” logic is updated in mgheatmap2 when col isn’t specified, but recenter is (backported to release 3.14)

Bug Fixes

  • calculateIndividualLogFC is updated to handle situations when $genes data.frame has column names that collide with statistics generated from differential expression, like pval, padg, and AveExpr. Thanks to @sandersen12 for the bug report.

sparrow 1.0 (2021-10-XX)

Enhancements

  • 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.

Breaking Changes from Pre-release

  • 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 the drop.unconformed = TRUE to retain the older behavior.