Question: PLINK gxe not reading covariate file
1
gravatar for jennavive00
4.6 years ago by
jennavive0020
United States
jennavive0020 wrote:

I am trying to conduct a GxE in PLINK using a covariate file but PLINK doesn't seem to be recognizing the file. Can someone tell me what I'm doing wrong?

plink --bfile omni --gxe --covar omni.txt

The covariate file omni.txt has the same # of observations as the .fam file and contains FID, IID, Covar1 coded like so...

FID  IID  Covar1

##   ##    1, 2, or -9

The log says that it reads the .bim and .fam files but doesn't even mention the covariate file.

covariate plink gxe • 1.9k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by jennavive0020

Hi,

Can you post or send me the .log file?

ADD REPLYlink written 4.6 years ago by chrchang5236.3k

PLINK v1.90b3j 64-bit (2 Apr 2015)
6 arguments: --bfile OMNI --covar omni.txt --gxe
Hostname: BR1
Working directory: W:\AIDGWAS
Start time: Thu Jun 18 11:18:48 2015

Random number seed: 1434651528
12245 MB RAM detected; reserving 6122 MB for main workspace.
608811 variants loaded from .bim file.
5582 people (2927 males, 2655 females) loaded from .fam.
5582 phenotype values loaded from .fam.

End time: Thu Jun 18 11:18:49 2015

ADD REPLYlink written 4.6 years ago by jennavive0020

This looks like a bug in the command-line parser/dispatcher; I will try to post a fix later today.

ADD REPLYlink written 4.6 years ago by chrchang5236.3k

Thank you! :)

ADD REPLYlink written 4.6 years ago by jennavive0020
1

Okay, I've investigated this; the bug is a missing error message.  PLINK should have printed "Error: --gxe requires a scalar phenotype." before exiting.  (Today's development build will do that.)

This brings us back to your dataset: --gxe does not handle case/control phenotypes, so you will need to use another analysis method.

ADD REPLYlink written 4.6 years ago by chrchang5236.3k
1

I'm a little confused. If it doesn't do case/control studies then what is it used for? It says here https://www.cog-genomics.org/plink2/order that --gxe is used for quantitative phenotype + case/control covariate association test

ADD REPLYlink written 4.6 years ago by jennavive0020
1

The covariate is case/control, but the main phenotype has to be continuous.

ADD REPLYlink written 4.6 years ago by chrchang5236.3k
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