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Procedure 1

    SNP data set: 1000 Genomes Pilot 1
    r2 threshold: 0.7
    Population panel: CEU
    Distance limit: 100
  • We substitute every marker for all its proxies and construct every possible pair for each file
  • Then we choose the common pairs to all files and construct a single one (p4.txt)
  • This file must be converted in plink format (just put a column after the other)
  • We run plink over each database looking for epistasis,
    plink --bfile bed_DB --epistasis --epi1 1 --epi2 1 --set-test --set sets.txt --allow-no-sex --out bed_DB_sets

$$ p = \phi \left( \frac{1}{\sqrt{k}} \sum_{i=1}^{k} \phi^{-1}(p_i) \right) $$ where $ \phi $ is the Normal distribution cumulative function.

genetica/bgscheme.txt · Last modified: 2020/08/04 10:58 (external edit)