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.