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cuelee / pleio

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pleioplot #4

Open sevi2018 opened 3 years ago

sevi2018 commented 3 years ago

Hi, I need some help with the R script I am getting the following error

Error in log10(sumstats[snp, paste(tr, "_p", sep = "")]) : non-numeric argument to mathematical function

I double checked the sumstats file and all traits pvalues are numeric. I also don't understand the error as should it be -log10 of pvalue?

Any idea what could be wrong?

Thanks in advance

cuelee commented 3 years ago

Hi, I've tried a few things so far and struggle to reproduce the bug yet. Currently, I am assuming that the pleiotropyPlot package you have is not up to date. To verify this possibility, could you completely uninstall and reinstall the pleiotropyPlot package and let me know if the error persists? This can be done by running the following commands in R:

remove.packages(‘pleiotropyPlot’)

source("http://jtilly.io/install_github/install_github.R")
install_github("cuelee/pleiotropyPlot")

Next, please check if you can generate an example PleiotropyPlot with example.R code, which you can find on the tutorial page (LINK).

If you still have the same problem, please create a reproducible example and share it with me(Email: cuelee@snu.ac.kr)? Then I can use the sample file to find the bug in the package.

You can check the source code of pleiotropyPlot on this github page (pleiotropyPlot github page).

Best, Cue

sevi2018 commented 3 years ago

Thanks for getting back to me and for sharing the code. That help me to understand where I got stucked and the cause. It was just a different column name btw different files that I did not notice before and running your code by pieces came out. Everything is working fine now!

On Fri, Sep 11, 2020 at 11:48 PM Cue Hyunkyu Lee notifications@github.com wrote:

Hi, I've tried a few things so far and struggle to reproduce the bug yet. Currently, I am assuming that your code is not up to date. To verify this possibility, could you completely uninstall and reinstall the pleiotropyPlot package and let me know if the error persists? This can be done by running the following commands in R:

remove.packages(‘pleiotropyPlot’)

source("http://jtilly.io/install_github/install_github.R")

install_github("cuelee/pleiotropyPlot")

Next, please check if you can generate an example PleiotropyPlot with example.R code, which you can find on the tutorial page (LINK) https://github.com/cuelee/pleiotropyPlot.

If you still have the same problem, please create a reproducible example and share it with me(Email: cuelee@snu.ac.kr)? Then I can use the sample file to find the bug in the package.

You can check the source code of pleiotropyPlot on this github page (pleiotropyPlot github page) https://github.com/cuelee/pleiotropyPlot.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/hanlab-SNU/pleio/issues/4#issuecomment-691399054, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJHJD3LVC3HYQ6FWOHTP4ZDSFLVQTANCNFSM4RD732KQ .

JYE-Lee commented 2 years ago

Hi @cuelee , I am getting the same error with this. I've checked that pleiotropyPlot packages is already updated. (version: pleiotropyPlot_0.0.0.9000)

Actually, I got this error since I updated the pleio with the command "git pull" a week ago. Before it, everything went fine with the same datasets. Can you help me with this again?

Thanks in advance!

cuelee commented 2 years ago

Hi JYE-LEE, Can you provide an example data set? I will test the data and try to find the cause of the problem. If okay, please send it to hl3565@cumc.columbia.edu.

Best Regards, Cue Hyunkyu Lee