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", "mm9"), keep_only_pass = FALSE, verbose = TRUE )
vcfs | VCF file paths. |
---|---|
samples | sample names for VCF files. |
genome_build | genome build version like "hg19". |
keep_only_pass | if |
verbose | if |
a MAF.
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) # }