R/load_data.R
extract_variants_from_matrix.Rd
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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 |
start_col | The name of the column that contains the start
position for each variant. Default |
end_col | The name of the column that contains the end
position for each variant. Default |
ref_col | The name of the column that contains the reference
base(s) for each variant. Default |
alt_col | The name of the column that contains the alternative
base(s) for each variant. Default |
sample_col | The name of the column that contains the sample
id for each variant. Default |
extra_fields | Optionally extract additional columns from the
object. Default |
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) #> -Reading #> -Validating #> -Silent variants: 206 #> -Summarizing #> --Possible FLAGS among top ten genes: #> TTN #> -Processing clinical data #> --Missing clinical data #> -Finished in 0.063s elapsed (0.061s 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")