[R] negative vector length when merging data frames

[Ana Marija]

Hi Jim,

I think one of the issue is that data frames are so big,
> dim(l4)
[1] 166941635         8
> dim(asign)
[1] 107371528         5

so my example would not reproduce the error

On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> Hi Ana,
> When I run this example taken from your email:
>
> l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
> chr1 13550  G  A b38 1:13550:G:A     0.375614 ENSG00000227232
> chr1 14671  G  C b38 1:14671:G:C     0.474708 ENSG00000227232
> chr1 14677  G  A b38 1:14677:G:A     0.699887 ENSG00000227232
> chr1 16841  G  T b38 1:16841:G:T     0.127895 ENSG00000227232
> chr1 16856  A  G b38 1:16856:A:G     0.627822 ENSG00000227232
> chr1 17005  A  G b38 1:17005:A:G     0.802803 ENSG00000227232",
> header=TRUE,stringsAsFactors=FALSE)
> asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> ENSG00000227232 chr1           1:10177:A:AC 10177     0.381708
> ENSG00000227232 chr1 rs145072688:10352:T:TA 10352     0.959523
> ENSG00000227232 chr1            1:11008:C:G 11008     0.218132
> ENSG00000227232 chr1            1:11012:C:G 11012     0.218132
> ENSG00000227232 chr1            1:13110:G:A 13110     0.998262
> ENSG00000227232 chr1  rs201725126:13116:T:G 13116     0.438572",
> header=TRUE,stringsAsFactors=FALSE)
> merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
>  [1] X1           X2           X3           X4           X5
> [6] variant_id   pval_nominal gene_id.LCL  gene         chr_pos
> [11] p.val.Retina
> <0 rows> (or 0-length row.names)
>
> It works okay, but there are no matches in the join. So I can't even
> guess what the problem is.
>
> Jim
>
> On Thu, Oct 24, 2019 at 9:33 AM Ana Marija <sokovic.anamarija using 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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