assigning cases and controls in plink
Quick question.
I am trying to assign cases in my study for association test with --make-pheno cases.list '*' option but program keeps telling me there's less than two phenotypes. My command line is:
plink --bfile cases --make-pheno cases.list '*' --assoc
My cases.list file has two columns with FID and IID like this:
18175 1
19233 1
19302 1
19342 1
19367 1
19427 1
19477 1
I am using plink 1.9
1 answer
plink --bfile cases --pheno casefilename.txt --make-bed --out newfilename
Above command is to update phenotype of cases which is coded by digit 2as explained below e.g.
18175 2
19233 2
19302 2
19342 2
19367 2
19427 2
19477 2
but if you wish to perform association testing(--assoc) you must include control samples as well along with the cases.
Log in to answer this question.
More posts like this
-
number of homozygotes with phenotype
written by ccagg
-
Processing WES VCF for case control GWAS analysis
written by sonsunjirachote •
-
instead of linear regression, do logistic regression plink prs tutorial.
written by beginner123 •
-
Plink Alternative Phenotype File Columns not being Read
written by dtlloyd •
-
PLINK ASSOC : Skipping --assoc/--model since less than two phenotypes are present.
written by Michal Nevo •
-
Covariates on non-phenotype fam file?
written by kstafford32 •
-
Plink error with reading phenotype file
written by MAPK
-
GWAS result too significant
written by yehchan57 •
-
Subset analyze of multiple sample file in PLINK 1.9
written by mike229lin •
-
How should the data be formatted to run an association mapping in PLINK?
written by beausoleilmo
