generateVariantTable: Make variant table from maf file

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Make variant table from maf file

Description

Make variant table from maf file

Usage

generateVariantTable(maf, use_syn = FALSE, extra_cols = c())

Arguments

maf	The MAF object
use_syn	Whether or not to include synonymous variants (default is FALSE, i.e. returns non-synonymous mutations only)
extra_cols	Vector of column names to include from the MAF file. If it's a named vector, the names will be used in the output table.

Value

A data frame containing the variant information

Author(s)

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
variantTable<-generateVariantTable(read.maf(maf))

MAFDash documentation built on April 1, 2022, 9:05 a.m.