I am trying to generate polygenic risk scores using the software PRSice. The base dataset has a quantitative phenotype. I want to generate the scores for subjects in a target dataset to test if PRS predicts drug response.
I used the following code to generate the scores through PRSice:
R --file=PRSice_v1.25.R -q --args plink ./plink_1.9_linux_160914 base ./crp_chrpos target ./genotype_maf1 binary.target F figname CRP clump.snps T slower 0.00000005 sinc 0.00005 supper 0.5 fastscore F no.regression T allow.no.sex T
After "Covary by generated dimensions" appeared in terminal, I received the following error message:
Error in file (file, "rt"): cannot open the connection Calls: read.table -> file Execution halted
I am not sure what file this error message is referring to, or how to remedy this. Any input or suggestions would be greatly appreciated.