choishingwan/PRSice

Is PRS.R2=Full.R2-Null.R2 correct?

Apprentice2 opened this issue · 2 comments

Thank you for developing a great tool.
I am developing a PRS for quantitative traits using PRSice-2. Of course, --beta, --binary-target F options were implemented it. I developed PRS with target data and the resulting summary file shows the following.

Phenotype Set Threshold PRS.R2 Full.R2 Null.R2 Prevalence Coefficient Standard.Error P Num_SNP

  • Base 5e-08 0.0149295 0.283942 0.273089 - 19.5742 2.03261 8.50818e-22 30

I am aware that PRS.R2=Full.R2-Null.R2. However, Full.R2-Null.R2=0.010853 in this result, which does not match 0.0149295 above. Why is this? I would appreciate it if you could enlighten me.

Thank you for you quick reply. I found a perfect match with the formula you gave me.