How To Create Cluster Files For Plink When Performing A Stratified Analysis On Three Different Population Datasets

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11.1 years ago

NB ▴ 960

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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ADD COMMENT • link updated 11.1 years ago by Istvan Albert 100k • written 11.1 years ago by NB ▴ 960

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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.

ADD REPLY • link 11.1 years ago by zx8754 11k

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yes, I do have the binary files but what do the clusters A,B,C stand for or represent ?

ADD REPLY • link 11.1 years ago by NB ▴ 960

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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.

ADD REPLY • link 11.1 years ago by zx8754 11k

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oh!! Thank you!

ADD REPLY • link 11.1 years ago by NB ▴ 960

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the question was deleted ? why ?

ADD REPLY • link 11.1 years ago by Pierre Lindenbaum 161k

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