Base file of PRSice software

[shubk]

I am using PRSice software for Polygenic risk score calculation of complex diseases like Type 2 Diabetes, Coronary artery disease. Input files required for analysis are Base file (example: TOY_BASE_GWAS.assoc ) and target file (binary files from plink for your target data). I am able to create target files using plink plug in from genome studio .,but Don't know how to create gwas association file for my phenotype like Type 2 Diabetes

[vivek_]

You'll have to search the highest powered GWAS of T2D and download the association results. That's the base file on which you are going to build the predictive model.

[shubk]

Thank you. I have downloaded association results from GWAS. The file has all required columns except effect size estimates, is there is any way to calculate it ? or is PRSice can run without effect size info in base file.
{PRSice requires the base file to contain information of the effective allele (--A1), effect size estimates (--stat)}

[vivek_]

Does it not have a Beta? If you have a z-score and p-value you can compute a beta from them using inverse probability transformation. You can read up on this online and get a formula to do so.

[shubk]

It does have a Beta/OR value for each SNP. Can this value be used instead of effect size?

[vivek_]

Beta is the effect size.