filterMAF | R Documentation |
This function filter the mutations in the MAF format using thresholds on various features
filterMAF( mafFilePath, 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 )
mafFilePath |
The path of the file 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) |
An object of class MAF with the filtered mutations
Mayank Tandon, Ashish Jain
library(MAFDash) maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash") filteredMAF <- filterMAF(mafFilePath = maf)
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