Question: Polygenic risk scoring using PRSice: Error in file(file, "rt") : cannot open the connection
0
gravatar for dam4l
2.5 years ago by
dam4l150
dam4l150 wrote:

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.

snp R prsice • 1.3k views
ADD COMMENTlink modified 2.3 years ago by bigfoot0 • written 2.5 years ago by dam4l150

I have the same problem. Did you solve it?

ADD REPLYlink written 2.3 years ago by charles50

I have not found a solution.

ADD REPLYlink written 2.3 years ago by dam4l150
0
gravatar for bigfoot
2.3 years ago by
bigfoot0
bigfoot0 wrote:

same problem.. any solution?

ADD COMMENTlink written 2.3 years ago by bigfoot0

I have not a found a solution.

ADD REPLYlink written 2.3 years ago by dam4l150
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