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BMGain
README.md
addStructs.m
calcGSS.m
calcMxGSS.m
combn.m
convertToPairInd.m
cutStruc2Inds.m
extractPlinkGenos.m
genos2Ct.m
getCTfromPlink.m
getPrevPerm.m
ismemberCellRow.m
prevPerm2Idx.m
readBim.m
readFam.m
runGssAnalysis.m
textprogressbar.m

README.md

gwis-stats

A demonstration of the novel statistics implemented in the paper "Goudey (2013) - GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS'

==How to run==

The main function is runGssAnalysis(plink_files, snp_list, GSS_type)

where plink_files is the filename of the PLINK binary files (.bed, .bim, .fam) without the final extension. This means all three files must share the same name.

snp_list is a list of snp identifiers corresponding to those in the .bim file Can either be

  • A 1D list of identifiers. We will then exhaustively search over all possible pairs of these SNPs.
  • A list of SNP pairs. Each of these will be explicityly evaluated.
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