MAF file is more recommended. In this function, we will mimic the MAF object from the key c(1, 2, 4, 5, 7) columns of VCF file.

read_vcf(
  vcfs,
  samples = NULL,
  genome_build = c("hg19", "hg38", "mm10"),
  keep_only_pass = FALSE,
  verbose = TRUE
)

Arguments

vcfs

VCF file paths.

samples

sample names for VCF files.

genome_build

genome build version like "hg19".

keep_only_pass

if TRUE, keep only 'PASS' mutation for analysis.

verbose

if TRUE, print extra info.

Value

a MAF.

See also

Examples

vcfs <- list.files(system.file("extdata", package = "sigminer"), "*.vcf", full.names = TRUE)
# \donttest{
maf <- read_vcf(vcfs)
maf <- read_vcf(vcfs, keep_only_pass = TRUE)
# }