read_vcf: Read VCF Files as MAF Object

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Read VCF Files as MAF Object

Description

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.

Usage

read_vcf(
  vcfs,
  samples = NULL,
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
  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

read_maf, read_copynumber

Examples

vcfs <- list.files(system.file("extdata", package = "sigminer"), "*.vcf", full.names = TRUE)

maf <- read_vcf(vcfs)
maf <- read_vcf(vcfs, keep_only_pass = TRUE)

ShixiangWang/sigminer documentation built on March 16, 2024, 12:30 p.m.