NEWS

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maftools 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