Scott Ritchie

Thanks @privefl , So the GWAS power relates to the power of the GWAS to predict the target trait in the data in which LDpred2 was run, rather than the...

Thanks for the advice, My plan is to iterate over shrink_corr = c(0.95, 0.9, 0.85, ..., 0.40) and use_MLE = c(TRUE, FALSE) at each shrink_corr, terminating in the first combination...

Hi Florian, Thanks for investigating. Yes - I'm primarily interested in predictive performance. We're in the progress of revising this preprint (https://www.medrxiv.org/content/10.1101/2024.08.22.24312440v3) to retrain the "metaPRS" (elastic-net of multiple LDpred2-derived...

No, we compute the LD directly from the training dataset. --- The GWAS summary statistics are on the GWAS Catalog with accession GCST90475667; http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90475001-GCST90476000/GCST90475667/harmonised/GCST90475667.h.tsv.gz has the file in the GWAS-catalog...

Also noting that INFO scores haven't been incorporated into the SNP QC as the training data are WGS not imputed genotypes.

Yes - The intuition here (which may very well be wrong) is the even though the SD plot looks awful, the SNPs that are kept will be the ones that...

Thanks - we'll test what happens, skipping LDpred2 auto when