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
)

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 0.084s elapsed (0.079s 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")