Function to filter the mutations — filterMAF • MAFDash

This function reads the the big MAF files in chunks and filter the mutations using various features

filterMAF(
  maf_file,
  chunk_lines = 10000,
  flag_genes = "default",
  save_name = NULL,
  no_filter = FALSE,
  grep_vcf_filter_col = "PASS",
  non_silent_only = FALSE,
  t_alt_min = 2,
  t_depth_min = 5,
  tumor_freq_min = 0.01,
  n_alt_max = 1,
  norm_freq_max = 0.01,
  gnomAD_AF_max = 0.001,
  AF_max = 0.001,
  ExAC_AF_max = 0.001,
  n_callers = 2,
  variant_caller = NULL
)

Arguments

maf_file: The path of the file containing the mutation information in the MAF format
chunk_lines: The number of lines to be read at once
flag_genes: The list of genes used as flag genes
save_name: The name and path of the output file to save filtered MAFs
no_filter: Flag to filter the MAF (Default no_filter=FALSE)
grep_vcf_filter_col: FILTER column (Default grep_vcf_filter_col="PASS")
non_silent_only: Flag to filter non slient SNVs only (Default non_silent_only=FALSE)
t_alt_min: Alt t min (Default t_alt_min=1)
t_depth_min: Depth t min (Default t_depth_min=20)
tumor_freq_min: Tumor Frequency Minimum (Default tumor_freq_min=0.05)
n_alt_max: Alt norm max (Default n_alt_max=1)
norm_freq_max: norm_freq_max (Default norm_freq_max=0.02)
gnomAD_AF_max: gnomAD_AF_max (Default gnomAD_AF_max=0.001)
AF_max: 1000 genome data AF_max (Default AF_max=0.001)
ExAC_AF_max: ExAC_AF_max (Default ExAC_AF_max=0.01)
n_callers: n_callers (Default n_callers=2)
variant_caller: variant_caller

Value

An object of class MAF with the filtered mutations

Author

Ashish Jain, Mayank Tondon

Examples

library(MAFDash)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
filteredMAF <- filterMAF(maf_file = maf)
#> Warning: Unknown or uninitialised column: `gnomAD_AF`.
#> Warning: Unknown or uninitialised column: `AF`.