pairRelation: Determine relationship between pairwise sample

Description Usage Arguments Value References

View source: R/pairRelation.R

Description

This function identifies relationship of pairwise sample [00: same patient | 10: X contaminate Y | 01 Y contaminate X | 11: both way contamination]

Usage

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pairRelation(sample_pairs,center_cutoff,source_cutoff,target_cutoff,
localPcomm_cutoff,region_cutoff,num_round_digit,output_path)

Arguments

sample_pairs

data frame, pairwise samples information

center_cutoff

numeric, cutoff to be classified as same subject samples (default: 0.5)

source_cutoff

numeric, cutoff to be classififed as source sample (default: 0.4)

target_cutoff

numeric, cutoff to be classified as target sample (default: 0.1)

localPcomm_cutoff

numeric, cutoff to manage high or low SNPs sharing between a pair of samples

region_cutoff

numeric, cutoff for case with low SNP sharing (default: 0.75)

num_round_digit

integer, rounding numeric up to this decimal point (default: 3)

output_path

character, output directory

Value

matrix, 2 columns containing pcommon and relation

References

TBA


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