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ChongWu-Biostat / aSPUpath2

The source codes for aSPUpath2 method. Visit www.wuchong.org/aspupath2.html for more details.
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Can't read the rds file #1

Closed tjmeyers closed 6 years ago

tjmeyers commented 6 years ago

Hi Chong,

I'm interested in trying out your program but I'm getting this error:

sumstat = readRDS(opt$sumstats) Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file 'NA', probable reason 'No such file or directory' Execution halted

I'm not familiar with the rds format-do you have any advice? I'm sorry for closing and re-opening this issue. Thanks.

ChongWu-Biostat commented 6 years ago

Hi, Thank you for your interest in our package. "rds" is an R format to store the data. I think your data format is not correct. You can change it to "rds" format and then it should work.

Let me know if you have any additional questions.

Thanks, Chong

tjmeyers commented 6 years ago

I ran your program using your own 'example.stat.rds' file and I still get this error.

ChongWu-Biostat commented 6 years ago

Sorry about that. Let me double check it.

ChongWu-Biostat commented 6 years ago

Can you check the following things:

  1. Install all the required packages;
  2. Put the weights into the correct directory.

I check the codes and there is no problem. Based on your error message, I think you put the files into the wrong directory and that's the reason you cannot use the software.

Thank you for your interest again! Let me know if you have any questions.

Thank you! Chong

ChongWu-Biostat commented 6 years ago

If you are familiar with R, it should be easy to modify it accordingly. You can download weights from TWAS FUSION website ( http://gusevlab.org/projects/fusion/).

Thanks, Chong

On Tue, May 15, 2018 at 4:59 PM, tjmeyers notifications@github.com wrote:

I checked the above but I still see the same error. Your Readme says the weights need to be in .rds format but GTEx provides their weights as .RDat. Do I need to convert them first?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ChongWu-Biostat/aSPUpath2/issues/1#issuecomment-389327127, or mute the thread https://github.com/notifications/unsubscribe-auth/AIU2vVH7TxHFLaK91SdPCFFAOZZf9FZmks5ty0_RgaJpZM4TnyX6 .

-- Chong Wu Biostatistics Ph.D. Candidate Phone: (612)516-2222 Division of Biostatistics Linked-In: www.linkedin.com/in/wuchong School of Public Health E-mail: chongwu@umn.edu University of Minnesota Website: www.wuchong.org

tjmeyers commented 6 years ago

My mistake, I was trying to run R as CMD BATCH instead of RScript. I located my version of RScript and the program runs now. Thanks.

ChongWu-Biostat commented 6 years ago

Good to know. Thank you for your interest in our software. Let me know if you have any additional questions.

Thanks, Chong

On Thu, May 17, 2018 at 3:58 PM, tjmeyers notifications@github.com wrote:

My mistake, I was trying to run R as CMD BATCH instead of RScript. I located my version of RScript and the program runs now. Thanks.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ChongWu-Biostat/aSPUpath2/issues/1#issuecomment-390009381, or mute the thread https://github.com/notifications/unsubscribe-auth/AIU2vcGjZsgWR5PYmgbUIeb_osaSfLOMks5tzeSIgaJpZM4TnyX6 .

-- Chong Wu Biostatistics Ph.D. Candidate Phone: (612)516-2222 Division of Biostatistics Linked-In: www.linkedin.com/in/wuchong School of Public Health E-mail: chongwu@umn.edu University of Minnesota Website: www.wuchong.org