Extract variants from a maf object

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Usage

extract_variants_from_maf(maf, extra_fields = NULL)

Arguments

maf

MAF object loaded by read.maf() from the 'maftools' package

extra_fields

Optionally extract additional columns from the maf object. Default NULL.

Value

Returns a data.table of variants from a maf which can be used to create a musica object.

Examples

maf_file <- system.file("extdata", "public_TCGA.LUSC.maf",
  package = "musicatk"
)
library(maftools)
maf <- read.maf(maf_file)
#> -Reading
#> -Validating
#> -Silent variants: 206 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   TTN
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.030s elapsed (0.028s cpu) 
variants <- extract_variants_from_maf(maf = maf)