extract_variants_from_matrix: Extract variants from matrix or data.frame like objects
In musicatk: Mutational Signature Comprehensive Analysis Toolkit

Description Usage Arguments Value Examples

Add Description

extract_variants_from_matrix(
  mat,
  chromosome_col = "Chromosome",
  start_col = "Start_Position",
  end_col = "End_Position",
  ref_col = "Tumor_Seq_Allele1",
  alt_col = "Tumor_Seq_Allele2",
  sample_col = "Tumor_Sample_Barcode",
  extra_fields = NULL
)

`mat`	An object that inherits from classes "matrix" or "data.frame" Examples include a matrix, data.frame, or data.table.
`chromosome_col`	The name of the column that contains the chromosome reference for each variant. Default `"Chromosome"`.
`start_col`	The name of the column that contains the start position for each variant. Default `"Start_Position"`.
`end_col`	The name of the column that contains the end position for each variant. Default `"End_Position"`.
`ref_col`	The name of the column that contains the reference base(s) for each variant. Default `"Tumor_Seq_Allele1"`.
`alt_col`	The name of the column that contains the alternative base(s) for each variant. Default `"Tumor_Seq_Allele2"`.
`sample_col`	The name of the column that contains the sample id for each variant. Default `"Tumor_Sample_Barcode"`.
`extra_fields`	Optionally extract additional columns from the object. Default `NULL`.

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

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)
variants <- extract_variants_from_matrix(mat = variants, 
chromosome_col = "chr", start_col = "start", end_col = "end", 
ref_col = "ref", alt_col = "alt", sample_col = "sample")