Extract variants from matrix or data.frame like objects

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)
#> -Reading
#> -Validating
#> -Silent variants: 206 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   TTN
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.028s elapsed (0.027s cpu) 
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"
)