How to Install PRISice

Question

[bastemku]

Hi. I 'm planning to estimate polygenic scores in my study. I have been struggling to install and initiate PRSice on my Linux. I have already downloaded, unzip the file but when I try to run it through the Linux terminal, it is not not running. I have tried to check info in the PRSice's website and Github, with no success. Any assistance?

[4galaxy77]

Did you follow the instructions on the github page? You don't need to unzip anything, you need to compile it.

[Sam]

Can you elaborate how is it not running? Did it give you some kind of error? What Linux did you use? Without these information, it is impossible for me to know what's going on.

[bastemku]

I'm using wsl in window. This is how I compiled it;

$git clone https://github.com/choishingwan/PRSice.git $cd PRSice $git clone https://github.com/choishingwan/PRSice.git $cd PRSice $mkdir build $cd build $cmake ../ make

Thereafter running this commandS in the Linux terminal to whether I will get something, but ended up getting this error: PRSice.R: command not found /PRSice_linux: command not found

Rscript PRSice.R \ --prsice PRSice_linux \ --base Height.QC.gz \ --target EUR.QC \ --binary-target F \ --pheno EUR.height \ --cov EUR.covariate \ --base-maf MAF:0.01 \ --base-info INFO:0.8 \ --stat OR \ --or \ --out EUR

[bastemku]

[Sam]

Command not found means you don't have the correct file. If you are compiling it yourself, then the executable should be bin/PRSice.

Assuming you are in the PRSice folder

mkdir build 
cd build
cmake ../
make
cd ../
./bin/PRSice -v

You can also find the PRSice.R in the PRSice folder.

Your error suggest that you cannot install optparse which is required by PRSice to parse the command. Though if you don't need plotting, you can skip the Rscript and use the executable directly (e.g. ./PRSice_linux)