Question: Polygenic Risk Score PLINK
0
gravatar for mzezza
3.7 years ago by
mzezza10
mzezza10 wrote:

Hi,

I have got my .assoc file with Odd Ratio for each SNP. Now I need help to understand how to calculate the Polygenic Risk Score on PLINK (command line).

ADD COMMENTlink modified 2.4 years ago by rse90 • written 3.7 years ago by mzezza10

What do you want to do? What is the goal of performing the Polygenic Risk Score analysis? Maybe you can look into PRSice which is a tool to automatically perform the PRS analysis for you.

ADD REPLYlink written 3.7 years ago by Sam3.0k

Hi, thanks for answer.

Do you know other ways to calculate the PRS ? Currently I can't run PRSice. Thanks for helping.

ADD REPLYlink written 3.7 years ago by mzezza10
1

Can you specific why you can't run PRSice?

ADD REPLYlink written 3.6 years ago by Sam3.0k

Hi,

I am running plink but getting only NA in the p-value column due to which i am getting empty output using PRSice. What can be the reasons for getting 'NA' value. I ran association analysis using --assoc command in plink on both ped/map and bim/fam/bed files.

Thanks

ADD REPLYlink written 2.4 years ago by rse90
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