PRSice 2

Question

[m.shoaib]

I am trying to calculate PRS in UKBB individuals for a binary trait (T2D). For that I am using the PRSice 2 software, This is how my code looks like,

Rscript PRSice.R \
--prsice PRSice_linux \
--dir . \
--base base.BMI.adjn.txt \
--target T2test# \
--snp rsID \
--chr CHR \
--bp BP \
--A2 A2 \
--A1 A1 \
--stat BETA \
--binary-target T \
--pvalue Pvalue \  
--out T2results

But I am getting error,

Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : " " is not a valid option, or does not support an argument Calls: parse_args -> parse_options -> getopt_options Execution halted

Please help me in solving this issue

Thanks

[Mensur Dlakic]

I don't know what this program is, but it would seem that the pound sign (#) will cause problems.

Answer 1

[Sam]

You have an extra space behind the \ in the --pvalue Pvalue \ line, which caused problem in parameter parsing.

[m.shoaib]

Hey @sam thank you for mentioning the error in my code.

Actually, I am delaing with a binary trait, so I have base file with effect size, target file (bed,bim,fam for cases) and pheno file with 'cases and controls with FID and IID.

But I am getting error,

There are a total of 1 phenotype to process

Start performing clumping

Clumping Progress: 100.00%
Number of variant(s) after clumping : 439

Processing the 1 th phenotype

Phenotype is a binary phenotype
0 control(s)
6113 case(s)

There are no control samples

So, my bed, bim and fam also requires both Cases and Control information? Sorry for my naive question. I am using PRSice for the first time

[Sam]

Do you only have cases? If you only got cases, then you can do the regression to optimize the p-value threshold. In that case, you will either need a known threshold, or extract a number of PRS to use for downstream without considering the threshold.

For the first option, use --fastscore --no-full --bar-levels <p-value> --no-regress, and for the second option, you can try --fastscore --no-regress.

[m.shoaib]

I have both cases and controls but the number of controls are significantly higher (cases=6113, controls=297701). I am not sure where is it required to provide controls info to the PRSice tool. In my understanding, I should have a target file with both cases and controls information. Moreover, I possibly need to mention the FIDs IIDs for both cases and controls in a single phenotype file (cases=2,controls=1) Please let me know if this the right way to proceed further?

[Sam]

All your cases and controls should be stored in the same genotype file. You should also provide a phenotype file containing all the case control information. --pheno is the way to provide

[m.shoaib]

Perfect. So what I understood my target files (bed,bim,fam) need to have both cases and controls information? Right?

[Sam]

correct, that is what's required

[m.shoaib]

thanks a lot!