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Table 1 Collapsing matrices

From: CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies

A
  SNP 2
0 1 2 3
SNP 1 0 0 0 0 0
1 0 1 1 1
2 0 1 0 3
3 0 1 3 3
B
  SNP 2
AA Missing Aa aa
SNP 1 AA 2 2 2 2
Missing 2 Missing Missing Missing
Aa 2 Missing 2 0
aa 2 Missing 0 0
C
  SNP 2
0 1 2 3
SNP 1 0 0 0 0 0
1 0 1 1 1
2 0 1 0 2
3 0 1 2 3
D
  SNP 2
AA Missing Aa aa
SNP 1 AA 2 2 2 2
Missing 2 Missing Missing Missing
Aa 2 Missing 2 1
aa 2 Missing 1 0
  1. (A) Machine representation of the default collapsing matrix. (B) Interpretation of the default collapsing matrix. Coding of input genotype follows PLINK convention, 0 (binary 00) for homozygote of minor allele, 1 (binary 01) for missing, 2 (binary 10) for heterozygote, and 3 (binary 11) for homozygote of major allele. After collapsing, the output pseudo-genotype is either 0, 2 or missing. The collapsing matrix is customizable by users, for example , an alternative collapsing matrix (C and D) will produce different pseudo-genotypes with allele coding 0, 1, 2 or missing