Please suggest any user friendly pipelines for the computation of Polygenic Risk Scores (PRS) on Microarray datasets?

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Abhijeet Singh

I don't have precise answer to that but I was wondering that calculation of scores or any other correlations are the post processing analyses and such kind of analysis can be done in the R/RStudio.

RStudio is user-friendly enough if you are familiar with the R language.

Gaurav Gupta

Thankyou Abhijeet Singh and Himanshu Joshi

for the answers, this has really helped. For R/R Studio it would be helpful but I am not much conversant with R. Although counting on the available instructions

For Impute.me is it authentic and how to upload multiple datasets?

Peymaneh Davoodi

Hi,

You can use R, PLINK, PRSice, Lassosum, LDpred, and also GTCA (sBLUP: summary-data-based BLUP analysis for genomic risk prediction) while each uses a specific algorithm to predict Polygenic Risk Score.

following article can help you more:

Article Tutorial: a guide to performing polygenic risk score analyses

Best regards

Lasse Folkersen

Hi Gaurav Gupta you are welcome to try out the new dockerhub for impute.me here:

https://hub.docker.com/repository/docker/lassefolkersen/impute-me

It sounds like your question fits well to the use case 2 as described in the readme. It may help you beyond just using the online web-server, because it sounds like you have a whole dataset to process (not just few people).