When trying to run snpnet, computeStats fails with
Error: Problem with `mutate()` column `stats_means`.
ℹ `stats_means = (HAP_ALT_CTS + HET_REF_ALT_CTS + 2 * TWO_ALT_GENO_CTS)/OBS_CT`.
✖ non-numeric argument to binary operator
My guess is that this is because of the presence of joined multiallelic sites causing PLINK to write cells with comma-separated numbers to some of the columns of the output of --geno-counts. In order to avoid the issue, I split the merged variants. However, then snpnet fails with
Error: --read-freq variant ID 'rs112422003' appears multiple times in main
So it looks like the user needs to make sure that the variants are split and have unique IDs. Is that correct? If so, then it would be nice if you could add this to the documentation somewhere.
When trying to run
snpnet,computeStatsfails withMy guess is that this is because of the presence of joined multiallelic sites causing PLINK to write cells with comma-separated numbers to some of the columns of the output of
--geno-counts. In order to avoid the issue, I split the merged variants. However, thensnpnetfails withSo it looks like the user needs to make sure that the variants are split and have unique IDs. Is that correct? If so, then it would be nice if you could add this to the documentation somewhere.