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Version 0.2

acidgsea 0.2.0 (2020-03-18)

Major changes:

  • Renamed package from “pfgsea” to “acidgsea”. Additional GSEA methods including the Broad GSEA Preranked algorithm and support for Jean Fan’s liger package are planned for a future update, so it no longer makes sense to pin the package name specifically to fgsea.
  • Reworked internally enriched gene set filtering and handoff. Affected functions: enrichedGeneSets, plotEnrichedGeneSets, and plotEnrichedUpset.

Minor changes:

  • convertToHuman: Updated working example to use Ensembl 99 release, as archived releases are currently unavailable via biomaRt until March 24, due to Ensembl server migration. See Ensembl website for details.
  • Updated minimal example gsea object.
  • Updated unit tests and working examples to reflect package name change.

acidgsea 0.2.1 (2020-05-12)

Minor changes:

  • Split out setValidity from setClass for S4 class definitions.
  • updateObject: Added support for ... and verbose arguments defined in the S4 generic.