How to use PRSice without a p-value (e.g data from PGSCatalog)

[frankMusacchia]

Hello, I am using PRsice with base data from PGScatalog. Nonetheless, I should use a --pvalue but it is not used in PGS catalog. The following are the first lines of a PGSCatalog file for ADHD disease rsID chr_name chr_position effect_allele other_allele effect_weight OR hm_source hm_rsID hm_chr hm_pos hm_inferOtherAllele rs139197039 10 10000797 A G -0.09709477124079369 0.90747 ENSEMBL rs139197039 10 9958834 rs139360817 10 10001085 A G -0.08110160143704147 0.9221 Unknown
rs7907011 10 100034296 T C 0.04009533056394215 1.04091 ENSEMBL rs7907011 10 98274539

as you can see there is no pvalue here to use. I went through a forum and someone tells to add a column with 0s. Yet, this idea conduct to false data and plots IMHO. Could you tell me what is the best thing to do in such cases? Thanks in advance Francesco

[choishingwan]

Effect sizes from PGS catalog were already optimized. As such you don't need to do clumping nor thresholding with them. You can either directly use PLINK to obtain the score, or as stated in other thread, give each SNP the same P-value and then use the following comment:

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

Such that PRSice will use all the SNPs to calculate the target PRS without doing thresholding or clumping.

Sam

On Tue, Jun 13, 2023 at 4:32 AM Francesco @.***> wrote:

Assigned #323 https://github.com/choishingwan/PRSice/issues/323 to @choishingwan https://github.com/choishingwan.

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[frankMusacchia]

Dear Sam, thanks for your prompt response. And thanks for suggesting how to do the analysis. Best regards Francesco Il giorno 14 giu 2023, alle ore 02:58, Shing Wan Choi @.***> ha scritto: Effect sizes from PGS catalog were already optimized. As such you don't

need to do clumping nor thresholding with them. You can either directly use

PLINK to obtain the score, or as stated in other thread, give each SNP the

same P-value and then use the following comment:

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

Such that PRSice will use all the SNPs to calculate the target PRS without

doing thresholding or clumping.

Sam

On Tue, Jun 13, 2023 at 4:32 AM Francesco @.***> wrote:

Assigned #323 https://github.com/choishingwan/PRSice/issues/323 to

@choishingwan https://github.com/choishingwan.

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