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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
187 stars 90 forks source link

No error but getting no plot #327

Closed zillurbmb51 closed 9 months ago

zillurbmb51 commented 1 year ago

prs_scz_bmi_maf_0.05_beta.log Hi, I ran PRSice without any error. At the end it shows "Begin plotting``\n" Current Rscript version = 2.3.3 I have downloaded the latest code from this github page. Should not it be 2.3.5? The point is it generates no plot. Even I added the --plot argument but still same. No plot. How could I plot the results? Attached is the log file. I am using HPC environment but it should not be an issue because other Rscripts that create plots, they work perfectly without any issue. Any help?

choishingwan commented 1 year ago

No plot will be generated if you use --no-regress as we cannot plot the performance of regression model that was not performed

SoumenMaity922 commented 1 year ago

Hi, I have written the following codes to run PRSice-2. It run without any error but it doesn't create any plot, it only creates three files EUR.prsice, EUR.best and EUR.all_score. PRSice --base Height.QC.gz --base-info INFO:0.8 --base-maf MAF:0.01 --target EUR.QC --pheno EUR.height --cov EUR.covariate --stat OR --or --out EUR --pvalue P --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5 --binary-target F. I am using the HPC environment through Mobaxterm. Please help.

choishingwan commented 9 months ago

Have answered the question in another issue.