extract_variants_from_matrix {musicatk} | R Documentation

## Extract variants from matrix or data.frame like objects

### Description

Add Description

### Usage

    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
    )

### Arguments

`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`.

### 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)
    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")

[Package musicatk version 1.2.0 Index]