Argument list too long - Githubissues

jean997 / cause

R package for CAUSE

https://jean997.github.io/cause/

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Argument list too long #47

Closed 931902655 closed 7 months ago

931902655 commented 7 months ago

Hi jean! I encountered this problem after running

X_clump <- X %>%
  rename(rsid = snp,
         pval = p1) %>%
  ieugwasr::ld_clump(dat = .,
                     clump_r2 = r2_thresh,
                     clump_p = pval_thresh,
                     plink_bin = "/usr/local/lib/R/site-library/plinkbinr/bin/plink_Linux", 
                     bfile = "/home/vee/code/pakage/EUR/EUR")

the following pic is the error 2b9119749f0178652a79bd731695fed Can you tell me how solve this problem? Thank you very much. Best regards.

jean997 commented 7 months ago

your error is coming from the ieugwasr package and not the CAUSE package so you should post this there: https://github.com/mrcieu/ieugwasr/

All I can tell you is that ld clumping failed. I would start by checking these things:

The bim/bed/fam files are where you think they are
The plink binary is where you think it is
your data is formatted correctly.

Look at the examples in the ieugwasr documentation and if you are still getting errors, post an issue on the ieugwasr issues page.