filter_maf_chunked: Function to filter the mutations

In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

Function to filter the mutations

Description

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

Usage

filter_maf_chunked(
  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(s)

Mayank Tondon, Ashish Jain

Examples

library(MAFDash)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
filteredMAF <- filter_maf_chunked(maf_file = maf)

MAFDash documentation built on April 1, 2022, 9:05 a.m.