"arguments must have same length" error in qqman::manhattan

Question

[raf.marcondes]

I'm getting the error below when trying to make a Manhattan plot in qqman from GWAS results (from gemma). It doesn't make any sense because all columns are in the same dataframe, so obviously they have the same length. I also already checked that chr, ps, and p_wald are all numeric, and that none has NAs. Thanks for any help!

> head(dat)
   chr                       rs    ps n_miss allele1 allele0    af        beta         se  logl_H1 l_remle       p_wald
1:   1 chr1_cl:20487[Thamno]C,T 20487      0       T       C 0.241  0.06871735 0.02126837 31.94490   1e+05 0.0034440570
2:   1 chr1_cl:23607[Thamno]A,G 23607      0       A       G 0.278  0.06240038 0.02013539 31.73593   1e+05 0.0047535890
3:   1 chr1_cl:23620[Thamno]C,T 23620      0       C       T 0.222 -0.11707830 0.02759205 34.71714   1e+05 0.0002647592
4:   1 chr1_cl:24502[Thamno]C,G 24502      0       G       C 0.667  0.08801808 0.02332899 33.61826   1e+05 0.0008856252
5:   1 chr1_cl:56337[Thamno]C,T 56337      0       C       T 0.444  0.04538745 0.01622219 30.89880   1e+05 0.0097585820
6:   1 chr1_cl:94431[Thamno]C,T 94431      0       T       C 0.222  0.06705353 0.02130109 31.74712   1e+05 0.0042208430

> manhattan(x=dat,
+           chr='chr',
+           bp='ps',
+           p='p_wald',
+           logp=T,
+           suggestiveline=F)
Error in tapply(d$SNP, d$CHR, length) : arguments must have same length
In addition: Warning message:
In manhattan(x = dat, chr = "chr", bp = "ps", p = "p_wald", logp = T,  :
  No SNP column found. OK unless you're trying to highlight.

Answer 1

[raf.marcondes]

Update in case anyone has the same issue: I solved it by specifying the snp argument, even though as the very warning message said it was supposed to be "OK unless you're trying to highlight"