How To Create Cluster Files For Plink When Performing A Stratified Analysis On Three Different Population Datasets
Hello,
I am trying to perform the Stratified analyses on three different population datasets using Cochran-Mantel-Haenszel test and Breslow-Day tests from PLINK. A cluster file "mycluster.dat" is needed but I am unable to understand the 3rd column from the format given on the PLINK website
F1 I1 A
F2 I1 B
F3 I1 B
F4 I1 C1
F5 I1 A
How can we create this file ?
Thank you
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Istvan Albert
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If you have binary plink files then open your FAM file on some editor (Excel?). Keep 1st and 2nd column and add 3rd column as your clusters: A, B, C etc. and save it as mycluster.dat. Use this file with --within option.
yes, I do have the binary files but what do the clusters A,B,C stand for or represent ?
They represent your population, as you mentioned you have "three different population dataset". So assign each individual to population: A, B, C, or however you wish to name them.
oh!! Thank you!
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