multipleSource: Identify true source from multisource contamination

In lpwgit/sampleContamination: Sample Contamination R Package

Description

This function uses Fisher exact test to filter multiple sources that contaminate a particular target sample

Usage

multipleSource(sample_pairs,VAFdata,VAFcov,VAF_cutoff,VAF_cutoff1,p.val_cutoff,output_path)

Arguments

sample_pairs	data frame, sample infomation
VAFdata	data frame, mutation VAF
VAFcov	data frame, mutation coverage
VAF_cutoff	numeric, minimum VAF (default: 0.002)
VAF_cutoff1	numeric, minimum VAF to be considered a source mutation (default: 0.05)
p.val_cutoff	numeric, pval cutoff to be considered a significant contamination source (default: 0.05)
output_path	character, output directory

Value

list, remaining paiwise sample relationship information after Fisher exact test that eliminates insignificant contamination pair

References

TBA

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