LD-pred 2 issue, All NAs in PRS file

[ShoaibBME]

Hi Sam, I am using LD pred 2 and used this tutorial, https://choishingwan.github.io/PRS-Tutorial/ldpred/ Actually, I have run the entire code with no errors but at the last step, where it is required to select one model. I am getting all NAs in the final PRS (pred_file) file, Same with other models, can you mention how to fix this? Thanks @choishingwan if(is.null(obj.bigSNP)){ obj.bigSNP <- snp_attach("EUR.QC.rds") } genotype <- obj.bigSNP$genotypes

calculate PRS for all samples

ind.test <- 1:nrow(genotype) pred_inf <- big_prodVec( genotype, beta_inf, ind.row = ind.test, ind.col = info_snp$_NUM_ID_)

[choishingwan]

Are you using your data or the one that's provided? And is your LDpred2 version the same as the one stated in the tutorial? The tutorial is more for introduction, and I haven't updated it to the latest version of LDpred2. For software specific query, I'd encourage you to contact the authors

Sam

On Mon, Jun 26, 2023, 11:55 AM ShoaibBME @.***> wrote:

Hi Sam, I am using LD pred 2 and used this tutorial, https://choishingwan.github.io/PRS-Tutorial/ldpred/ Actually, I have run the entire code with no errors but at the last step, where it is required to select one model. I am getting all NAs in the final PRS (pred_file) file, Same with other models, can you mention how to fix this? Thanks @choishingwan https://github.com/choishingwan if(is.null(obj.bigSNP)){ obj.bigSNP <- snp_attach("EUR.QC.rds") } genotype <- obj.bigSNP$genotypes calculate PRS for all samples

ind.test <- 1:nrow(genotype) pred_inf <- big_prodVec( genotype, beta_inf, ind.row = ind.test, ind.col = info_snp$NUM_ID)

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