inst/NEWS.md
In maftools: Summarize, Analyze and Visualize MAF Files

CHANGES IN VERSION 2.6.05

Improve clinicalEnrichment odd-ratio interpretation. Issue: 633 In earlier versions, odds-ratio indicated the odds of observing WT in the group of interest compared to Mutant. From this update, odds-ratio indicate the odds of observing mutant in the group of interest compared to wild-type. This way is much intuitive and easier interpret. See issue 633 for details. P-values and other details are unaffected.
Changes in how Multi_Hit are reported. By default two distinct types of mutations in the same gene or same patient were classified as Multi_Hit (e.g; Missense + Splice_Site = Multi_Hit; Missense + Missense = Missense). This update onward, regardless of type of mutations, if there are >1 mutations in the same gene of same patient, they are classified as Multi_Hit (e.g; Missense + Splice_Site = Multi_Hit; Missense + Missense = Multi_Hit). Issue: 347 347

Updated TCGA TMB. All variants from MC3 results are restricted and harmonized to Agilent 35.8 MB capture kit. See ?tcgaCompare for details. Issue: 612
Added SIMC1 protein to domain database. Issue: 616
Added sampleOrder1 and sampleOrder2 arguments to coOncoplot. Issue: 592
Added gene_mar outer_mar argument to coOncoplot. Issue: 260
Added sample size warning messages to mafCompare. Issue: 602
Added cohortFontSize and axisFontSize to tcgaCompare