Changes in version 2.18.0                        

NEW FUNCTIONS

  - pathways and plotPathwaysfor summarizing & visualizing pathways
    Issue: 956
  - coGisticChromPlot for plotting two GISTIC objects side-by-side. PR
    by biosunsci 954
  - readGistic can take gistic output directory as an input. PR by
    biosunsci 954

BUG FIXES

  - Bug fixes while processing custom pathways
  - Bug fix in oncoplot for drawing borders. 958
  - Bug fix in plotSignatures for hardcoded axis limits. 949
  - Bug fix in mafSurvival legend when samples argument is give. 937
  - Bug fix in subsetMaf while handling only CNV events. 908
  - Error handling when no deep/shallow CNV events found. 899
  - Bug fix in oncoplot for duplicated values in gene list. 889

ENHANCEMENTS

  - Added argument collapsePathway to oncoplot. Issue: 956
  - Improved annovarToMaf with better handling of indels and
    Variant_Type. Issue: 940
  - Include absolute contribution of each signature in extractSignatures
    output. Issue: 939
  - Added tsbToPIDs for custom names in oncoplot. Issue: Issue: 936
  - Added DSEL protein to the database. Issue: 933
  - Added MUC3A protein to the database. Issue: 932
  - Added showOnlyPathway argument to oncoplot
  - Added pathdb argument to PlotOncogenicPathways. Issue: 923
  - Emit warnings when fishers test can not be performed during
    somaticInteractions. Issue: 921
  - Added leftMar and topMar arguments to somaticInteractions. Issue:
    913
  - Added toptBarLims argument to oncoplot. Issue: 910
  - Added data argument to lollipopPlot function. Issue: 894
  - Added sortByM1 and sortByM2 argument to coOncoplot. Issue: 888
  - Added arguments leftBarVline, leftBarVlineCol, rightBarVline,
    rightBarVlineCol topBarHline topBarHlineCol to oncoplot. Issue: 874
  - Added revPal argument to somaticInteractions. Issue: 859
  - Fix legend and color codes for numeric annotations in oncoplot.
    Issue: 363