I am doing Polygenic Risk Score analysis for microarray data with a specific trait. I am facing problem to understand the outputs generated by PRSice application (v1.25) and looking forward for any guidance or help for the same.
Questions are: 1. How to set individual PRS quantile (specific traits for a sample) wrt. to GWAS dataset. Can we find single quantile for a individual ? 2. How to calculate candidate threshold and R2 value? Is there any datasheet generated while running PRSice for quantiles for a single sample (trait)? 3. How to choose a best fit p-val for a given trait for finding PRS (pruning is preferred or any p-val can be given as threshold cut-off clumping ?
- How to analyze the PRS for a single trait (TARGET+Phenotype) of a sample wrt. GWAS dataset (BASE)
If any other suggestions done during this analysis ? Any guidance, I sincerely welcome.
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