Tool: Plink- creating cluster file when control data set same for each cluster
0
gravatar for alyssaiclay
3.8 years ago by
alyssaiclay0 wrote:

Hello,

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.

 

 

 

ADD COMMENTlink written 3.8 years ago by alyssaiclay0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1278 users visited in the last hour