Model Performance R2

[m-mews]

If I understand correctly, the best.validation.result is the correlation between the actual and predicted phenotype and the square if the percent of the phenotype that is explained by the genetic model. However, the correlation in the validation$results.table pheno and best.pgs is dramatically different from the best.validation.result (ex. 0.44 vs. 0.72). Can you please clarify why this difference exists? Thank you in advance!

[tshmak]

I can't replicate the difference using the toy example I provided in README.md. Also, it is supposed to be the simple Pearson's correlation and not R2 that is being calculated.