Read VCF Files as MAF Object

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", "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)
# \donttest{
maf <- read_vcf(vcfs)
#> Reading file(s): /home/runner/work/_temp/Library/sigminer/extdata/test1.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test3.vcf
#> It seems /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf has no normal VCF header, try parsing without header.
#> Annotating Variant Type...
#> Downloading https://zenodo.org/record/10360995/files/human_hg19_gene_info.rds to /home/runner/work/_temp/Library/sigminer/extdata/human_hg19_gene_info.rds
#> Annotating mutations to first matched gene based on database of hg19...
#> Transforming into a MAF object...
#> -Validating
#> --Non MAF specific values in Variant_Classification column:
#>   Unknown
#> -Summarizing
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.024s elapsed (0.038s cpu) 
maf <- read_vcf(vcfs, keep_only_pass = TRUE)
#> Reading file(s): /home/runner/work/_temp/Library/sigminer/extdata/test1.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test3.vcf
#> It seems /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf has no normal VCF header, try parsing without header.
#> Annotating Variant Type...
#> Annotating mutations to first matched gene based on database of hg19...
#> Transforming into a MAF object...
#> -Validating
#> --Non MAF specific values in Variant_Classification column:
#>   Unknown
#> -Summarizing
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.022s elapsed (0.036s cpu) 
# }