filter_maf_chunked | R Documentation |
This function reads the the big MAF files in chunks and filter the mutations using various features
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 )
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 |
An object of class MAF with the filtered mutations
Mayank Tondon, Ashish Jain
library(MAFDash) maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash") filteredMAF <- filter_maf_chunked(maf_file = maf)
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