I also tried left_join but I got: Error: std::bad_alloc
> df3 <- left_join(l4, asign, by = c("chr","pos"))
Error: std::bad_alloc
> dim(l4)
[1] 166941635 8
> dim(asign)
[1] 107371528 5
On Wed, Oct 23, 2019 at 5:32 PM Ana Marija <sokovic.anamar...@gmail.com> wrote:
>
> 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
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