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==UCLA Sib-pair Analysis== * Sib-pair data: for every affect indiv take methyl frequency and substract the methyl frequency of an unaffected sibling * Null-pair data: for every inter-family pair, take the methyl frequency of mother and substract the methyl frequency of the father or take the methyl frequency of child and substract methyl frequency of parent * User perl's Statistics::TTest module. Test whether the means are significantly different by p<=0.05 between the sib-pair set and the null pair set ./cpgMatrixSibPairTTest.pl sample_info.txt sites_KW_unsignif0.10n5 > fam_filtered_sibpairTstat.LOG & * [[File:cpgMatrixSibPairTTest.txt]] * Outputs: '''File too big, see /home/ddiep/UCLA_Analysis/sibpairTstat.KWunsignif0.10n5.matrix (meangenemachine)''' * Hierarchical clustering at sib pair significant sites: [[File:sibpairHclust_UCLA.pdf]] There are two branches and all affected individuals are on one branch (some unaffected individuals are also on same branch).
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