Extract Non-Synonymous Mutations from MAF — get_maf

Filters a MAF GenomicRanges object to retain only non-synonymous mutations, including both SNVs and InDels and splice site variantss.

Variant Class: SNV, insertion, deletion

Non-Synonymous Classifications: Missense_Mutation, Nonsense_Mutation, Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Nonstop_Mutation, Translation_Start_Site, Splice_Site, Splice_Region

Note, this function was designed to be run downstream of read_maf_file()

Usage

get_maf_nonsynonymous(
  maf_gr,
  variant_class = c("SNV", "insertion", "deletion"),
  include_splice = TRUE
)

Arguments

maf_gr: GenomicRanges object containing MAF data with metadata columns
variant_class: Character vector of variant class to include. Default: c("SNV", "insertion", "deletion")
include_splice: Logical, whether to include splice site variants (default: TRUE)

Value

A GenomicRanges object containing only non-synonymous mutations