Polygenic Risk Score PLINK

0

Entering edit mode

8.0 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 • 8.2k views

ADD COMMENT • link updated 6.7 years ago by rse ▴ 100 • written 8.0 years ago by mzezza ▴ 10

0

Entering edit mode

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 8.0 years ago by Sam ★ 4.8k

0

Entering edit mode

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 8.0 years ago by mzezza ▴ 10

1

Entering edit mode

Can you specific why you can't run PRSice?

ADD REPLY • link 8.0 years ago by Sam ★ 4.8k

0

Entering edit mode

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 6.7 years ago by rse ▴ 100

Login before adding your answer.