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.
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.