search

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
185 stars 87 forks source link

[BUG] Liability scale conversion returns full model result, not R2 attributable to PRS #277

Closed JoniColeman closed 2 years ago

JoniColeman commented 3 years ago

With PRSice 2.3.3, when using --prevalence to convert observed-scale Nagelkerke R2 to liability scale, observed-scale R2 is reported for the PRS alone, but liability-scale R2 is reported for the PRS + covariates.

choishingwan commented 3 years ago

Update should be live now. Do let me know if you still encountered the same error.

JoniColeman commented 3 years ago

This works, but the .prsice file is still listing the Full R2, not the PRS R2 (the summary file is fine)

choishingwan commented 3 years ago

Ya, that was kinda by design. It shouldn’t be too hard to implement it for .prsice file, but for now I think I will keep it that way as am busy rebuilding it from scratch. Will keep in mind that it is sobering we want to do

On Tue, 28 Sep 2021 at 7:40 AM, Joni Coleman @.***> wrote:

Reopened #277 https://github.com/choishingwan/PRSice/issues/277.

— You are receiving this because you modified the open/close state.

Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/277#event-5373222791, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYWK7VDJESFBT47NEJTUEGSTJANCNFSM5EMOJG7A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Dr Shing Wan Choi Instructor Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

JoniColeman commented 3 years ago

Ok - but the label of that field in the .prsice file is "R2.adj", when it is in fact the full R2 of the model - that's inconsistent with what's reported in the documentation, right?

choishingwan commented 3 years ago

oh, I'll have to change that than. Haven't update the documentations for a while now. Thanks!

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.