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jean997 / cause

R package for CAUSE
https://jean997.github.io/cause/
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p_value of X? #12

Closed Dawn0502 closed 3 years ago

Dawn0502 commented 3 years ago

Hi, I merged the X as the instruction in the tutorial. And when I perform step 3: LD pruning with these code:

X_clump <- IntelandICV %>% rename(rsid = snp) %>% ieugwasr::ld_clump(dat = ., clump_r2 = r2_thresh, clump_p = pval_thresh, plink_bin = genetics.binaRies::get_plink_binary(), bfile = ref_path)

The result returned an error Error: Can't rename columns that don't exist. x Column p_value doesn't exist. I was confused that if this p_value belongs to the merged dataset X or something else?

Thanks for all your help!

Best Regards, Dawn

jean997 commented 3 years ago

Hi Dawn, I'm sorry I missed this issue, I hope you got it figured out.

It looks like an error with the ld_clump function in ieugwasr which expects specific column names for p-value. Here is the reference for that function: https://mrcieu.github.io/ieugwasr/reference/ld_clump.html I find the error weird because the ld_clump expects your p-value column to be called "pval" not "p_value" The error about not renaming columns that don't exist suggests that IntelandICV doesn't have a column named snp. Jean