PLINK analysis for case/control studies
Hi,
I have genotype data from Affymetrix. I want to look at my cases and controls using gPLINK to see what SNPs are present and I want to find which SNPs are unique in cases compared to controls for comparison. What kind of QC steps and other analysis I should do to get the results I am looking for?
1 answer
How many samples and SNPs do you have?
You should read this article (Quality control procedures for genome-wide association studies). They are showing how to use PLINK to do your QC.
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So you are trying to see if a particular SNP is captured in the case but not in control? If that is the case, the plink (not gPlink) command should be something like
You will then have a file that tells you whether if a snp has higher missingness in case / control (something similar to the thing you want) If a SNP is "unique" to case / control, then you should definitely get it. If you don't have the binary files but only the ped files, the you can replace bfile with file.
Thank you very much. This is helpful.