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Old 08-06-2013, 08:25 AM   #1
Location: England

Join Date: Jan 2013
Posts: 16
Default PLINK association covariants issue

Hi all,

I am trying to do a GWAS in PLINK.

I am running
plink --file [file] --linear --covar [covariant-file] --out [name]
which give me an acceptable output with a subset of my desired covariants. However, I need to have both age and age^2 of the patients as covariants within the final analysis.

When I include both of these as covariants, PLINK provides 'NA' as the output for all association tests. This is a 'feature' of PLINK:

The NA issue arises due to excessive correlation of two covariants, is my understanding, so as age and age^2 are inexorably linked, the --vif alteration cannot get around it.

I know that GWAS using these two covariants have been performed in PLINK successfully, based on some GWAS paper methods sections, but I cannot seem to work out a way to get this to work.

Does anyone have any suggestions as to how I may bypass this feature, I am sure that there are sound statistical logics as to why bypassing this may not be the soundest thing to do, but my analyses are going into a multi-centre meta-analysis, so I really don't get any say in what models are in use at this stage.

Any suggestions would be (extremely) gratefully received.
rjohnp is offline   Reply With Quote

'na', covariants, gwas, plink

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