GWAS with KEGG pathway analysis

Question

[kkp5232]

I am new with pathway analysis. I am very confused with plink set-based tests: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml

I am not sure if this is correct progress. My goal is to find the p-value with my SNPs, subjects' age, and subjects' cognitive scores. I am confused how to include the subjects' cognitive scores into this plink? Maybe I am wrong about plink. Is there any other ways to do it?

I have been write the programs to analysis pathway. I just want to see if there is any other ways by using software out of there.

Thank you for your time in advance of time!

[kautilya]

Can you explain a bit more as to what exactly is your objective for using PLINK.

From your question it seems that you are looking for association between SNPs and students cognitive score. In this case you can divide the students cognitive scores into certain classes like(high, medium, low) depending on their value, this then becomes your phenotype for PLINK.

Get you data into the plink input format and run the association tests(like chi-square or fishers) using plink options. This will give you a p-value for each SNP which can help you shortlist SNPs which might be associated with cognitive ability. You can apply a cutoff like 0.05 for the p-value.

[kkp5232]

I am trying my best. My goal is to find p-value for each SNP. Right now, in my Rscript program, I wrote like this: lm(cog_score~SNP+age) to find p-value. However, it took me forever. So I am wondering if this PLINK set-based tests will be work for this progress?

If yes, I am confused most with this --set-test --set my.set from http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#set.. Also I am confused how to included cognitive score. Is that "my.set" for? If yes, how to make it?