PRSice2 --base-maf and --base-info flag issue

[charlisech]

Describe the bug When following the PRS tutorial, the flags --base-maf and --base-info can not recognize the input and cannot find corresponding columns in the base file.

Error Log

2020-07-03 13:17:40
./PRSice_mac \
    --A1 A1 \
    --A2 A2 \
    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
    --base height.QC \
    --base-info INFO:0.8 \
    --base-maf MAF:0.01 \
    --binary-target F \
    --bp BP \
    --chr CHR \
    --clump-kb 250 \
    --clump-p 1.000000 \
    --clump-r2 0.100000 \
    --cov-file EUR.cov \
    --interval 5e-05 \
    --lower 5e-08 \
    --missing MEAN_IMPUTE \
    --model add \
    --or  \
    --out EUR \
    --pheno-file EUR.height \
    --pvalue P \
    --score avg \
    --seed 86459283 \
    --snp SNP \
    --stat OR \
    --target EUR.QC \
    --thread 1 \
    --upper 0.5

Warning: INFO field not found in base file,will ignore INFO filtering 
Error: Invalid argument passed to --base-maf: MAF:0.01! Threshold must be numeric 

To Reproduce The code used is straight from the tutorial.

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

Additional context All the files used are from the tutorial. In the base file, there are MAF and INFO columns, not sure why PRsice wasn't able to detect them. Below is the first couple lines of the base file, where you can see the MAF and INFO column.

[echoheqian]

Hi, are you figure out this problem?

[choishingwan]

Have you got similar problem? If so, please send me the full log and command use. Preferably also include the header of your summary statistic file.

[Hybert9108]

Hi, I got the same problem using Mac. I used the example data from the PRS tutorial (https://choishingwan.github.io/PRS-Tutorial/prsice/). I also tried other systems including win and linux, and they all worked well.

haibotang@tanghaibodeMacBook-Pro PRS % Rscript PRSice.R \ --prsice PRSice_mac \ --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 PRSice 2.2.11.b (2019-10-16) https://github.com/choishingwan/PRSice (C) 2016-2019 Shing Wan (Sam) Choi and Paul F. O'Reilly GNU General Public License v3 If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019) 2022-07-07 15:55:17 ./PRSice_mac \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base Height.QC.gz \ --base-info INFO:0.8 \ --base-maf MAF:0.01 \ --binary-target F \ --clump-kb 250 \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --cov EUR.covariate \ --interval 5e-05 \ --lower 5e-08 \ --or \ --out EUR \ --pheno EUR.height \ --seed 137444216 \ --stat OR \ --target EUR.QC \ --thread 1 \ --upper 0.5

Warning: INFO field not found in base file, will ignore INFO filtering Error: Invalid argument passed to --base-maf: MAF:0.01! Threshold must be numeric

Thank you so much!

[choishingwan]

2 2.11b is I so old, please use the latest version

On Thu, Jul 7, 2022, 4:12 AM Hybert9108 @.***> wrote:

Hi, I got the same problem using Mac. I used the example data from the PRS tutorial (https://choishingwan.github.io/PRS-Tutorial/prsice/). I also tried other systems including win and linux, and they all worked well.

@.*** PRS % Rscript PRSice.R --prsice PRSice_mac --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 PRSice 2.2.11.b (2019-10-16) https://github.com/choishingwan/PRSice (C) 2016-2019 Shing Wan (Sam) Choi and Paul F. O'Reilly GNU General Public License v3 If you use PRSice in any published work, please cite: Choi SW, O'Reilly PF. PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data. GigaScience 8, no. 7 (July 1, 2019) 2022-07-07 15:55:17 ./PRSice_mac --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 --base Height.QC.gz --base-info INFO:0.8 --base-maf MAF:0.01 --binary-target F --clump-kb 250 --clump-p 1.000000 --clump-r2 0.100000 --cov EUR.covariate --interval 5e-05 --lower 5e-08 --or --out EUR --pheno EUR.height --seed 137444216 --stat OR --target EUR.QC --thread 1 --upper 0.5

Warning: INFO field not found in base file, will ignore INFO filtering Error: Invalid argument passed to --base-maf: MAF:0.01! Threshold must be numeric

Thank you so much!

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/210#issuecomment-1177232846, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYQ7OPHI6QYKHUZPOO3VS2GQJANCNFSM4OP657GQ . You are receiving this because you were assigned.Message ID: @.***>

[Hybert9108]

Perfect！Thanks a lot！