sigminer (version 1.2.5)

read_vcf: Read VCF Files as MAF Object

Description

Read VCF Files as MAF Object

Usage

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

read_maf, read_copynumber

Examples

# NOT RUN {
vcfs <- list.files(system.file("extdata", package = "sigminer"), "*.vcf", full.names = TRUE)
# }
# NOT RUN {
maf <- read_vcf(vcfs)
maf <- read_vcf(vcfs, keep_only_pass = FALSE)
# }