Question: PRSice polygenic score with only controls
0
gravatar for aldoc
2.6 years ago by
aldoc10
aldoc10 wrote:

Hi,

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$PHENO))[1] == "1" & levels(as.factor(prof$PHENO))[2] ==  :
  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,

polygenic snp prsice • 1.5k views
ADD COMMENTlink modified 2.6 years ago by coleman_jonathan410 • written 2.6 years ago by aldoc10
3
gravatar for coleman_jonathan
2.6 years ago by
European Union
coleman_jonathan410 wrote:

This a known bug - no regression still requires a non-missing phenotype. I recommend you run PRSice with a dummy phenotype file as you describe and the no regression option on

ADD COMMENTlink written 2.6 years ago by coleman_jonathan410

Thanks! I tried it with two different "random phenotype" files, and gives the same results. Just for future reference, the whole command was:

R --file=PRSice_v1.25.R -q --args plink PRSice_v1.25/plink_1.9_linux_160914 base referencefile.txt target myplinkfile slower 0 sinc 0.01 supper 0.5 report.best.score.only F no.regression T report.individual.scores T covary F pheno.file randomphenotypes.txt

The final output (after automatic cleanup) was two files: PROFILES.nosex and PRSice_SCORES_AT_ALL_THRESHOLDS.txt.

Best,

ADD REPLYlink written 2.6 years ago by aldoc10
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