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. The name of the column that contains the chromosome reference for each variant. Default "Chromosome". The name of the column that contains the start position for each variant. Default "Start_Position". The name of the column that contains the end position for each variant. Default "End_Position". The name of the column that contains the reference base(s) for each variant. Default "Tumor_Seq_Allele1". The name of the column that contains the alternative base(s) for each variant. Default "Tumor_Seq_Allele2". The name of the column that contains the sample id for each variant. Default "Tumor_Sample_Barcode". 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)