read_maf_flexible: Read MAF from ANNOVAR OR MAF input

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

Read MAF from ANNOVAR OR MAF input

Description

Automatically detects filetype from

Usage

read_maf_flexible(
  path_mutations,
  refBuild = NULL,
  path_clindata = NULL,
  filetype = c("AUTO", "ANNOVAR", "MAF")
)

Arguments

path_mutations	path to mutation file (string)
refBuild	which reference version is being used
path_clindata	path to clinical annotation file (string)
filetype	what type of filetype do we expect (string). If "AUTO" will automatically guess the filetype using [guess_genomic_mutation_filetype()]

Value

one of MAF, ANNOVAR, VCF, OTHER

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.