Make variant table from maf file

generateVariantTable(maf, use_syn = FALSE, extra_cols = c())

Arguments

maf: The MAF object
use_syn: Whether or not to include synonymous variants (default is FALSE, i.e. returns non-synonymous mutations only)
extra_cols: Vector of column names to include from the MAF file. If it's a named vector, the names will be used in the output table.

Value

A data frame containing the variant information

Author

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
variantTable<-generateVariantTable(read.maf(maf))
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.254s elapsed (0.229s cpu) 
#> Not outputting these columns: gnomAD_AF, AF