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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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Is PRS.R2=Full.R2-Null.R2 correct? #321

Closed Apprentice2 closed 1 year ago

Apprentice2 commented 1 year ago

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

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.

choishingwan commented 1 year ago

It's 1-(1-full)/(1-null)

On Sun, Jun 11, 2023, 1:29 AM Apprentice2 @.***> wrote:

Assigned #321 https://github.com/choishingwan/PRSice/issues/321 to @choishingwan https://github.com/choishingwan.

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Apprentice2 commented 1 year ago

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