[R] negative vector length when merging data frames

[Ana Marija]

Hello,

I have two data frames like this:

> head(l4)
    X1    X2 X3 X4  X5  variant_id pval_nominal     gene_id.LCL
1 chr1 13550  G  A b38 1:13550:G:A     0.375614 ENSG00000227232
2 chr1 14671  G  C b38 1:14671:G:C     0.474708 ENSG00000227232
3 chr1 14677  G  A b38 1:14677:G:A     0.699887 ENSG00000227232
4 chr1 16841  G  T b38 1:16841:G:T     0.127895 ENSG00000227232
5 chr1 16856  A  G b38 1:16856:A:G     0.627822 ENSG00000227232
6 chr1 17005  A  G b38 1:17005:A:G     0.802803 ENSG00000227232
> head(asign)
              gene  chr                chr_pos   pos p.val.Retina
1: ENSG00000227232 chr1           1:10177:A:AC 10177     0.381708
2: ENSG00000227232 chr1 rs145072688:10352:T:TA 10352     0.959523
3: ENSG00000227232 chr1            1:11008:C:G 11008     0.218132
4: ENSG00000227232 chr1            1:11012:C:G 11012     0.218132
5: ENSG00000227232 chr1            1:13110:G:A 13110     0.998262
6: ENSG00000227232 chr1  rs201725126:13116:T:G 13116     0.438572
> m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  :
  negative length vectors are not allowed
> sapply(l4,class)
          X1           X2           X3           X4           X5   variant_id
 "character"  "character"  "character"  "character"  "character"  "character"
pval_nominal  gene_id.LCL
   "numeric"  "character"
> sapply(asign,class)
        gene          chr      chr_pos          pos p.val.Retina
 "character"  "character"  "character"  "character"  "character"

Please advise as to why I am getting this error when merging?

Thanks
Ana