mixingRatio: Calculate contamination level

In lpwgit/sampleContamination: Sample Contamination R Package

Description

This function calculates contamination level, ratio of VAF_target to VAF_source

Usage

mixingRatio(VAFdata,VAFcov,sample_pairs,final_rel,VAF_cutoff,VAF_ignore,
ALL_flag,output_path,sameSubject)

Arguments

VAFdata	data frame, mutation VAF
VAFcov	data frame, mutation coverage
sample_pairs	data frame, pairwise samples information
final_rel	data frame, relation information
VAF_cutoff	numeric, minimum VAF (default: 0.002)
VAF_ignore	numeric, ignore variant less than this cutoff (default: 0.2)
ALL_flag	logical, TRUE: calculate mixing ratio for all pairwise samples, FALSE: calculate mixing ratio for contamination pairwise samples
output_path	character, output directory
sameSubject	logical, TRUE: calculate contamination level for same subject pairs (default: FALSE)

Value

matrix containing source sample, target sample, relation, contamination level, flip_flag

References

TBA

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