filterMAF2: Function to filter the mutations

In ashishjain1988/MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

Function to filter the mutations

Description

This function filter the mutations in the MAF format using thresholds on various features

Usage

filterMAF2(
  maf,
  flag_genes = "default",
  save_name = NULL,
  no_filter = FALSE,
  norm_alt_max = 1,
  t_alt_min = 1,
  t_depth_min = 20,
  tumor_freq_min = 0.05,
  norm_freq_max = 0.02,
  gnomAD_AF_max = 0.001,
  AF_max = 0.001,
  ExAC_AF_max = 0.001,
  n_callers = 2,
  variant_caller = NULL
)

Arguments

maf	Dataframe object containing the mutation information in the MAF format
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)
norm_alt_max	Alt norm max (Default norm_alt_max=1)
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)
norm_freq_max	norm_freq_max (Default norm_freq_max=0.02)
gnomAD_AF_max	Maximum allele frequency in gnomAD database (Default gnomAD_AF_max=0.001)
AF_max	Maximum allele frequency in 1000 genome database (Default AF_max=0.001)
ExAC_AF_max	Maximum allele frequency in ExAC database (Default ExAC_AF_max=0.01)
n_callers	Minimum number of callers identified mutation. (Default n_callers=2)
variant_caller	Name of variant caller to be used or "consensus" to apply filter based on 'n_callers' (Default variant_caller=NULL)

Value

An object of class MAF with the filtered mutations

Author(s)

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
mafDF <- read.table(maf, sep='\t', header=TRUE, fill = TRUE, quote="\"", stringsAsFactors = FALSE)
filteredMAF <- filterMAF2(maf = mafDF)

ashishjain1988/MAFDash documentation built on Feb. 9, 2023, 9:54 p.m.