Tool: Plink- creating cluster file when control data set same for each cluster
gravatar for alyssaiclay
4.6 years ago by
alyssaiclay0 wrote:


I am creating a cluster file to use in plink for stratified analyses/breslow-day tests/ homogeneity tests.  I read on the plink website that:  This file should have a similar structure to the alternate phenotype file. The clusters can be coded either numerically or as strings:

     F1 I1  A
     F2 I1  B
     F3 I1  B
     F4 I1  C1
     F5 I1  A
     F6 I1  C2
     F7 I1  C2

Here, individuals would be grouped in four groups:

     Cluster A:  F1/I1  F5/I1
     Cluster B:  F2/I1  F3/I1
     Cluster C1: F4/I1  
     Cluster C2: F6/I1  F7/I1

All individuals in the file should be assigned to a single cluster in the cluster file. 

This is all fine.  Except this last statement.  What if my control set stays the same within each strata.

Example: Age1 vs. entire control set =Custer A

Age2 vs. entire control set= Cluster B

Age 3 vs. entire control set= Cluster C

Meaning this control set is in each cluster- but I can only assigned an individual to 1 cluster..

Has anyone else had this problem...suggestions? Thank you.




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