Changes in version 2.8.05                        

BUG FIXES

  - Fix error in mafSurvGroup while checking for mutants in geneSet.
    Added minMut argument to mitigate. Issue: 741

ENHANCEMENTS

  - Fix the order of features and added colors for the lines in
    forestPlot. Thanks @biosunsci PR: 761
  - Added pwLineCol and pwLineWd for controlling the line color and line
    width around the pathways in oncoplot. Issue: 759
  - Added ORthr and featureLvls arguments to plotEnrichmentResults.
    Issue: 715
  - Added pseudoCountargument to MafCompare for avoiding Inf values in
    estimated OR. Issue: 718
  - Added compressargument to write.mafSummary and now the output
    includes clinical data as well. Issue: 720

                        Changes in version 2.8.0                        

NEW FUNCTIONS

  - cancerhotspots Genotype known cancer hotspots from the tumor BAM
    file
  - bamreadcounts extract nucleotide counts for targeted variants from
    the BAM file.
  - maftools now natively loads TCGA cohorts. tcgaAvailable and tcgaLoad
    will display and load the desired cohorts.
  - Added MAF constructor function
  - Added maf2mae for converting MAF to MultiAssayExperiment class
    objects Issue: 640 293 Discussion: 285
  - Added plotProtein and mafbarplot

ENHANCEMENTS

  - Added protein domains for the gene ALMS1. Issue: 705
  - Added titv_col argument to oncoplot. Issue: 702
  - Added protein domains for the gene FAM205A. Issue: 701
  - oncoplot can now summarize variant_classifications similar to
    cBioPortal style. Issue: 686
  - Added pathway support for mafCompare() or clinicalEnrichment().
    Issue: 681
  - Added default title for side and topbar plots to oncoplot. Issue:
    682
  - Added annotationOrder argument to coOncoplot. Issue: 676
  - Added plot argument to survGroup. Thank you OmarElAshkar PR: 674
  - Added rmFlags argument to read.maf. Issue: 668
  - Added path_order argument to oncoplot for custom ordering of
    pathways on oncoplot.
  - Added geneMar argument to coBarplot. Issue: 260

BUG FIXES

  - coOncoplot not allowing more than one additional feature. Issue: 675