I am trying to use the PRSice package to calculate polygenic risk scores for samples, but when I try to include a covariate file in the analysis, an error occurs with the --cov flag in my command line. The code and the error message are as shown below.
$ Rscript PRSice.R --dir . --prsice ./PRSice_linux --base pf75.assoc.linear --target pividoripruned --pheno-file fev075.txt --no-clump --cov cov.cov --thread 1 --stat BETA --beta --binary-target F
The error is
Error in getopt_options(object, args) :
Error in getopt(spec = spec, opt = args) : long flag "cov" is ambiguous
Calls: parse_args -> parse_options -> getopt_options
Execution halted
How can I solve the problem? Your help is very much appreciated! Thank you!
1 answer
I have the same problem like this. I want to ask how to sovle the problem.
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which version are you using? I am pretty sure 2.3.3 should work with the about settings