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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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How to apply to Discovery dataset #290

Closed ArashLab closed 2 years ago

ArashLab commented 2 years ago

Hi, I am a bit confused about how to use PRSice-2 to calculate the Polygenic Risk Score for the discovery dataset.

I have a Case/Control dataset (binary phenotype) and I split samples into 70% (base dataset) and 30% (target dataset) I used the plink --assoc for the base dataset and then use PRSice to calculate PRS for the target dataset.

I have a separate dataset (discovery) without the phenotype. How can I calculate PRS for the discovery dataset? It seems that PRS requires phenotype for the target data and complaints if no phenotype is provided.

choishingwan commented 2 years ago

You can use --no-regress --no-full --bar-levels XXX --fastscore where XXX is the best threshold you found via your CV

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.