Question: How To Create Cluster Files For Plink When Performing A Stratified Analysis On Three Different Population Datasets
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gravatar for Nandini
6.1 years ago by
Nandini780
London
Nandini780 wrote:

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

deleted-post • 4.5k views
ADD COMMENTlink modified 6.1 years ago by Istvan Albert ♦♦ 80k • written 6.1 years ago by Nandini780

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 REPLYlink written 6.1 years ago by zx87547.1k

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

ADD REPLYlink written 6.1 years ago by Nandini780
1

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 REPLYlink written 6.1 years ago by zx87547.1k

oh!! Thank you!

ADD REPLYlink written 6.1 years ago by Nandini780

the question was deleted ? why ?

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Pierre Lindenbaum118k
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