[R] negative vector length when merging data frames

[Ana Marija]

thanks but I would need solution in R

On Wed, Oct 23, 2019 at 6:31 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> I don't have it installed - that was merely a suggestion. I notice
> that both data.table and dplyr packages are mentioned as possibilities
> for "merge big datasets in r". Apparently the best way to do it if you
> have a database manager is to read the two datasets into tables and do
> the join via SQL or whatever language is available.
>
> Jim
>
> On Thu, Oct 24, 2019 at 10:17 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >
> > no can you please send me an example how the command would look like in my case?
> >
> > On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon <drjimlemon using gmail.com> wrote:
> > >
> > > 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
> > > > > >
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