Changes in version 2.22.0                        

BUG FIXES

  - Bug fix in using keepGeneOrder in coOncoplot(). Issue: 1061
  - Bug fix in using selectedPathways in oncoplot(). Issue: 1041
  - Add an error message when bai files are missing sampleSwaps().
    Issue: 1028
  - Bug fix in tmb while handling multiple MAFs. Issue: 1018
  - Handle missing NAs while sub-setting for ranges. Issue: 1013
  - Better error handling when zero mutated samples are encountered in
    clinicalEnrichment. Issue: 1010
  - MAJOR: read.maf by default coerces clinical data columns to
    character. This bug fix avoids it and is auto detected. Issue: 997

ENHANCEMENTS

  - Better handling of color codes for continuous variable annotations
    1053
  - Add right_mar to gisticOncoPlot1043
  - Added PPDPFL to protein domain database Issue: 1025
  - Better sorting of oncoplot with collapsePathway
  - Changed default background for oncoplot from gray to #ecf0f1
  - Changed default signature database to SBS_v3.4 (from legacy)
  - Update tmb function

BREAKING CHNAGES

  - Column order required for pathways() function changed from
    Pathway,Gene to Gene,Pathway. Issue: 1041

NEW FUNCTIONS

  - gisticCompare() for comparing two GISTIC objects
  - segSummarize() for summarizing DNAcopy segments