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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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Not getting any plot #52

Closed SoumenMaity922 closed 9 months ago

SoumenMaity922 commented 1 year ago

Hi, I follow all the steps described in the tutorial session. I downloaded the data(base and target) at the beginning of QC ( didn't download the QC data). I have run the following code PRSice --base Height.QC.gz --target EUR.QC --binary-target F --pheno EUR.height --cov EUR.covariate --base-maf MAF:0.01 --base-info INFO:0.8 --stat OR --or --out EUR It creates three files EUR.best, EUR.prsice, and EUR.summary. But it doesn't create any plot. Why? Any help? I am using the HPC environment and it uses the PRSice-2.3.5 version.

choishingwan commented 9 months ago

The PRSice executable itself does not generate plot. For plot generation, you need to use PRSice.R which is a wrapper of PRSice.