PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Cites methods from "PLINK: A Tool Set for Whole-Genome ..."
...Some software packages (e.g. plink Purcell et al. 2007) have been specifically developed to both handle such huge data sets and to directly perform statistical analyses on the data....
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Cites background from "PLINK: A Tool Set for Whole-Genome ..."
...9’s core functional domains are unchanged from that of its predecessor—data management, summary statistics, population stratification, association analysis, identity-by-descent estimation [1] —and it is usable as a drop-in replacement in most cases, requiring no changes to existing scripts....
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Cites methods from "PLINK: A Tool Set for Whole-Genome ..."
...Two estimates have been used: one based on the variance of additive genetic values (diagonal of the SNP-derived GRM) and the other based on SNP homozygosity (implemented in PLINK).(25) Let (1 – pi) 2 þ pi(1 – pi)F, 2pi(1 – pi)(1 – F), and pi 2 þ pi(1 – pi)F be the frequencies of the three genotypes of a SNP i and let hi 1⁄4 2pi(1 – pi)....
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"PLINK: A Tool Set for Whole-Genome ..." refers methods in this paper
...There is an option to use a Euclidean IBS distance metric in place of the standard metric of proportional sharing; classical MDS based on a Euclidean distance metric is numerically identical to principal-components analysis, which forms the basis of other methods.(10) Finally, PLINK also supports an IBS-based “nearestneighbor” analysis to detect outlying individuals who do not belong with any major cluster in the sample....
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