Description Usage Arguments Value References
This function identifies relationship of pairwise sample [00: same patient | 10: X contaminate Y | 01 Y contaminate X | 11: both way contamination]
1 2 | pairRelation(sample_pairs,center_cutoff,source_cutoff,target_cutoff,
localPcomm_cutoff,region_cutoff,num_round_digit,output_path)
|
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 |
matrix, 2 columns containing pcommon and relation
TBA
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