I want to know why the correlation of PRS obtained by plink and PRSice is low.
Firstly, I used plink --clump. The parameters are same as PRSice process.
plink --bfile HCP --clump gwas --clump-p1 0.00145 --clump-r2 0.1 --clump-kb 250
Then, I used the clumped snp (include OR and effect allele) as input to compute score:
plink --bfile HCP --score gwas_0.00145P_clumped 2 4 6
I obtained the PRS of every subjects by plink.
PRSice calculations follow the manual strictly.
Then I checked the correlation between PRS from plink and PRSice.Pearson correlation coefficient is 0.49 ,p =0.