extract_variants_from_maf {musicatk}

R Documentation

Extract variants from a maf object

Description

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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)
variants <- extract_variants_from_maf(maf = maf)

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