run_sampleContamination: Main function to run sample contamination analysis

In lpwgit/sampleContamination: Sample Contamination R Package

Description

This function detects sample contamination base on variant allele frequency (VAF) and variant coverage

Usage

run_sampleContamination(data_path, output_path, config_file="config.txt",
rmSNPcv_cutoff=0,manualsetPara=FALSE,manual_localPcomm=10,manual_center=50,filterCOV=0)

Arguments

data_path	character, mutation VAF and coverage file directory
output_path	character, output directory
config_file	character, configuration file
rmSNPcv_cutoff	numeric, TRUE: filter SNPs with low covariance of coefficient (COV) (default: FALSE)
manualsetPara	logical, TRUE: manual setting base on distribution of pairwise samples commonality (default: FALSE)
manual_localPcomm	numeric, manual setting of localPcomm for low or high contamination (default: 10)
manual_center	numeric, manual setting of center cutoff for same subject determination (default: 50)
filterCOV	numeric, filter mutation below this cutoff

Value

list, containing pcomm, center cutoff, target cutoff, source cutoff, region cutoff and number of sample

References

TBA

lpwgit/sampleContamination documentation built on May 21, 2019, 7:51 a.m.