I'm trying to calculate polygenic scores using PRSice; my dataset contains only controls (PLINK-coded as "-9"). When running PRSice, I get the following message:
Error in if (levels(as.factor(prof$PHENO)) == "1" & levels(as.factor(prof$PHENO)) == : missing value where TRUE/FALSE needed Execution halted
In principle, this happens because PRSice is trying to get different levels for the phenotype in order to do a regression and compare cases vs controls. But even when specifying "no.regression T" or "no.regression T report.individual.scores T", the program gives the same output. Has anyone experienced/solved this before?
A brute-force alternative could be to insert "random" phenotypes (namely, to use both "1"s and "2"s for every pheno), and just neglect the regression outputs. But this is not quite orthodox...
Any help is appreciated. Thanks,