I am using R-3.6.1
and these libraries:
library(data.table)
library(dplyr)
On Wed, Oct 23, 2019 at 6:54 PM Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>
> On 23/10/2019 7:04 p.m., Ana Marija wrote:
> > 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
>
> Looks like bugs in whatever package you're finding "left_join" in (and
> previously "merge"). Are those from dplyr and base? Showing us
> str(lr), str(asign), and sessionInfo() would be helpful.
>
> Duncan Murdoch
>
> >> 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
> >
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
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