[R] negative vector length when merging data frames

[Jim Lemon]

Yes. Have you tried the bigmemory package?

Jim

On Thu, Oct 24, 2019 at 10:08 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> 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
> > >
> > > ______________________________________________
> > > R-help using 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.