Customize Base Dataset

[JinhanZhu1]

Hey,

The documentation of PRSice mentioned that the base dataset should be a file indicate the effect size for a SNPs, usually a GWAS summary stats. Does the PRSice/PRset provide the flexibility that I can use other files such as PRScsx's output which already did LD pruning and didn't have P-value column.

Thanks for your help!

[choishingwan]

For now, no. But you can generate a "fake" pvalue column with the same p value, then do

--no-clump --fastscore --bar-levels 1

Though if you are doing PRS CSx, you might considering directly calculating the PRS with plink --score

Sam

On Thu, Aug 17, 2023, 2:02 PM Zhujh @.***> wrote:

Hey,

The documentation of PRSice mentioned that the base dataset should be a file indicate the effect size for a SNPs, usually a GWAS summary stats. Does the PRSice/PRset provide the flexibility that I can use other files such as PRScsx's output which already did LD pruning and didn't have P-value column.

Thanks for your help!

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/336, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYWDZ3PJPJ2LZDHJCYDXVZMBTANCNFSM6AAAAAA3UN4HAU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[JinhanZhu1]

For now, no. But you can generate a "fake" pvalue column with the same p value, then do … --no-clump --fastscore --bar-levels 1 Though if you are doing PRS CSx, you might considering directly calculating the PRS with plink --score Sam On Thu, Aug 17, 2023, 2:02 PM Zhujh @.> wrote: Hey, The documentation of PRSice mentioned that the base dataset should be a file indicate the effect size for a SNPs, usually a GWAS summary stats. Does the PRSice/PRset provide the flexibility that I can use other files such as PRScsx's output which already did LD pruning and didn't have P-value column. Thanks for your help! — Reply to this email directly, view it on GitHub <#336>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYWDZ3PJPJ2LZDHJCYDXVZMBTANCNFSM6AAAAAA3UN4HAU . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks for the information! I also want to ask can I use PRSet to calculate competitive P-value while inserting fake P-column in base dataset? My guess is that using a fake P-value for SNPs in base dataset will not impact the output of competitive P-value, but still want to double check!

Best, Jinhan

[choishingwan]

I've never tested PRSet with effect sizes trained on whole genome (e.g. from PRScsx) so I am not sure if that violates our assumptions. But yes, in theory you can still run PRset with fake pvalue as by default we don't want to do p value thresholding with set base PRS and only use the pvalue for set based clumping

On Thu, Aug 17, 2023, 5:54 PM Zhujh @.***> wrote:

For now, no. But you can generate a "fake" pvalue column with the same p value, then do … <#m-6541004676179019652> --no-clump --fastscore --bar-levels 1 Though if you are doing PRS CSx, you might considering directly calculating the PRS with plink --score Sam On Thu, Aug 17, 2023, 2:02 PM Zhujh @.> wrote: Hey, The documentation of PRSice mentioned that the base dataset should be a file indicate the effect size for a SNPs, usually a GWAS summary stats. Does the PRSice/PRset provide the flexibility that I can use other files such as PRScsx's output which already did LD pruning and didn't have P-value column. Thanks for your help! — Reply to this email directly, view it on GitHub <#336 https://github.com/choishingwan/PRSice/issues/336>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYWDZ3PJPJ2LZDHJCYDXVZMBTANCNFSM6AAAAAA3UN4HAU https://github.com/notifications/unsubscribe-auth/AAJTRYWDZ3PJPJ2LZDHJCYDXVZMBTANCNFSM6AAAAAA3UN4HAU . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks for the information! I also want to ask can I use PRSet to calculate competitive P-value while inserting fake P-column in base dataset? My guess is that using a fake P-value for SNPs in base dataset will not impact the output of competitive P-value, but still want to double check!

Best, Jinhan

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/336#issuecomment-1683029563, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYXLRBDYY3BS4G7XFQDXV2HKXANCNFSM6AAAAAA3UN4HAU . You are receiving this because you commented.Message ID: @.***>