pairPCommon: Pairwise Sample Function

In lpwgit/sampleContamination: Sample Contamination R Package

Description

4 different functions for pairwise sample

Usage

pairPCommon(VAFdata,VAF_cutoff,num_round_digit,n)
pairShare(VAFdata,VAF_cutoff,n)
pairList(VAFdata,n,del)
pairCommList(SNPcomm,n)

Arguments

VAFdata	data frame, mutation VAF
VAF_cutoff	numeric, minimum VAF
num_round_digit	numeric, number of rounding decimal digit (default: 3)
n	numeric, number of sample
SNPcomm	matrix, output from the calling of pairPCommon(VAFdata,VAF_cutoff,num_round_digit,n)
del	character, file delimiter

Details

pairPCommon: calculates pcommon

pairShare: counts number of common SNPs

pairList: generates all pairwise sample list

pairCommList: tabulates pcommon for all pairwise samples

Value

pairPCommon: matrix, nxn pcommon, n: number of sample

pairShare: matrix, nxn number of common snps

pairList: vector, all pairwise samples

pairCommList: list, all pairwise samples and their pcommon values

References

TBA

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