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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 11 months ago

youniwerse commented 12 months 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 12 months 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 11 months 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!