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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 0.089s elapsed (0.082s cpu)
variants <- extract_variants_from_maf(maf = maf)