Skip to contents

Version 0.7

AcidGSEA 0.7.0 (2022-04-27)

Major changes:

  • Split out basejump dependencies into individual packages.
  • Added support for multiple contrasts: plotNES, plotGeneSet, results.
  • export method now confirms to BiocIO approach, using con argument.
  • RankedList: Tightned up Ensembl reference genome filtering, checking for gene identifiers from primary chromosomes, to avoid unwanted averaging of values from haplotype scaffold gene identifiers. Also added support for proteinCodingOnly, to enable analysis of protein coding genes only, which is disabled by default.
  • Reworked our internal Gene2Symbol handling for plot functions.

Minor changes:

  • FGSEAList and RankedList: Reworked default formals for keyType and value.
  • Added basejump as a dependency to R Markdown template.
  • Relaxed gene-to-symbol class checks for RankedList S4 class.
  • Improved rich text formatting for CLI messages, where applicable.
  • Added an additional assert check for gene identifier overlap prior to internal fgsea handoff.
  • plotLFC: Improved labeling of axes.
  • prepareGeneSetFiles: Reworked file name detection for MSigDb.
  • Improved internal code for returning results for all contrasts.