Tabulate SNVs by trinucleotide contextSource:
This function produces trinucleotide-context-specific SNV counts from MAF data for input to mutational signature extraction tools. Output can be tailored to meet formatting requirements of MutationalPatterns or deconstructSigs, which are probably similar to formats used by other tools.
a cancereffectsizeR-style MAF data table
BSgenome reference genome (for looking up trinucleotide contexts)
Default FALSE. When TRUE, only mutations private to each sample are included in counts, in order to reduce the influence of selection. (If you load more MAF data into the CESAnalysis later, recurrency may change.)
"MutationalPatterns" or "deconstructSigs"