How to apply to Discovery dataset

[ArashLab]

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]

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

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