Polygenic Risk Score PLINK

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7.4 years ago

mzezza ▴ 10

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).

plink polygenic risk score risk score SNP scoring • 8.0k views

ADD COMMENT • link updated 6.2 years ago by rse ▴ 100 • written 7.4 years ago by mzezza ▴ 10

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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 REPLY • link 7.4 years ago by Sam ★ 4.7k

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Hi, thanks for answer.

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

ADD REPLY • link 7.4 years ago by mzezza ▴ 10

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Can you specific why you can't run PRSice?

ADD REPLY • link 7.4 years ago by Sam ★ 4.7k

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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 REPLY • link 6.2 years ago by rse ▴ 100

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