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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
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Error can't open base file #344

Closed youniwerse closed 1 year ago

youniwerse commented 1 year ago

Hi,

I'm trying to use a GWAS summary data as the base file. But I keep receiving the following error message:

youwang@Yous-MacBook-Pro PRsice_mac % Rscript PRSice.R --prsice PRSice_mac --base "/Users/youwang/Desktop/PUMC/GFAP_analysis/shunyi_data/HDL_EA" Error: Cannot open file - /Users/youwang/Desktop/PUMC/GFAP_analysis/shunyi_data/HDL_EA

Below is the first 10 rows of the GWAS summary data I'm trying to use. Is it because it's not formatted properly?

X SNP_hg19 ID A1 A2 BETA SE N P Freq.A1.1000G.EAS SNP 14235 10:113913222 rs2297991 C T -0.04947 0.007203 47456 6.52e-12 0.7579 10:113913222:T:C 14239 10:113933886 rs2255141 G A -0.04921 0.007199 47456 8.15e-12 0.7579 10:113933886:A:G 14241 10:113940329 rs2792751 C T -0.04941 0.007208 47456 7.14e-12 0.7629 10:113940329:T:C 14243 10:113944271 rs2419604 G A -0.05399 0.008813 30661 9.02e-10 0.7609 10:113944271:A:G 14244 10:113949664 rs10787429 C T -0.05316 0.008835 30661 1.77e-09 0.7609 10:113949664:T:C 14245 10:113950418 rs7096937 C T -0.05359 0.008829 30661 1.28e-09 0.7619 10:113950418:T:C 18190 11:61552680 rs174537 T G -0.0484723 0.009278 25759 1.75e-07 0.5675 11:61552680:G:T 18191 11:61557803 rs102275 C T -0.0439944 0.008215 33279 8.54e-08 0.5675 11:61557803:T:C 18193 11:61569830 rs174546 T C -0.0457092 0.00821 33279 2.59e-08 0.5665 11:61569830:C:T 18194 11:61570783 rs174547 C T -0.0458525 0.008211 33279 2.35e-08 0.5665 11:61570783:T:C

choishingwan commented 1 year ago

Make sure you're path is right.

It said it cannot find the file. And maybe don't use the double quote

On Wed, Sep 20, 2023, 4:32 PM youniwerse @.***> wrote:

Hi,

I'm trying to use a GWAS summary data as the base file. But I keep receiving the following error message:

@.*** PRsice_mac % Rscript PRSice.R --prsice PRSice_mac --base "/Users/youwang/Desktop/PUMC/GFAP_analysis/shunyi_data/HDL_EA" Error: Cannot open file - /Users/youwang/Desktop/PUMC/GFAP_analysis/shunyi_data/HDL_EA

Below is the first 10 rows of the GWAS summary data I'm trying to use. Is it because it's not formatted properly?

X SNP_hg19 ID A1 A2 BETA SE N P Freq.A1.1000G.EAS SNP 14235 10:113913222 rs2297991 C T -0.04947 0.007203 47456 6.52e-12 0.7579 10:113913222:T:C 14239 10:113933886 rs2255141 G A -0.04921 0.007199 47456 8.15e-12 0.7579 10:113933886:A:G 14241 10:113940329 rs2792751 C T -0.04941 0.007208 47456 7.14e-12 0.7629 10:113940329:T:C 14243 10:113944271 rs2419604 G A -0.05399 0.008813 30661 9.02e-10 0.7609 10:113944271:A:G 14244 10:113949664 rs10787429 C T -0.05316 0.008835 30661 1.77e-09 0.7609 10:113949664:T:C 14245 10:113950418 rs7096937 C T -0.05359 0.008829 30661 1.28e-09 0.7619 10:113950418:T:C 18190 11:61552680 rs174537 T G -0.0484723 0.009278 25759 1.75e-07 0.5675 11:61552680:G:T 18191 11:61557803 rs102275 C T -0.0439944 0.008215 33279 8.54e-08 0.5675 11:61557803:T:C 18193 11:61569830 rs174546 T C -0.0457092 0.00821 33279 2.59e-08 0.5665 11:61569830:C:T 18194 11:61570783 rs174547 C T -0.0458525 0.008211 33279 2.35e-08 0.5665 11:61570783:T:C

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youniwerse commented 1 year ago

Hi,

Just moved the base file to the folder where PRSice is located and it works. Seems to be the issue of the path.

Thank you!