[R] how to find number of unique rows for combination of r columns

[Ana Marija]

I tried it but I got this error:
> udt <- unique(dt[c("chr", "pos", "gene_id")])
Error in `[.data.table`(dt, c("chr", "pos", "gene_id")) :
  When i is a data.table (or character vector), the columns to join by
must be specified using 'on=' argument (see ?data.table), by keying x
(i.e. sorted, and, marked as sorted, see ?setkey), or by sharing
column names between x and i (i.e., a natural join). Keyed joins might
have further speed benefits on very large data due to x being sorted
in RAM.

On Fri, Nov 8, 2019 at 8:58 AM Gerrit Eichner
<gerrit.eichner using math.uni-giessen.de> wrote:
>
> Hi, Ana,
>
> doesn't
>
> udt <- unique(dt[c("chr", "pos", "gene_id")])
> nrow(udt)
>
> get close to what you want?
>
>   Hth  --  Gerrit
>
> ---------------------------------------------------------------------
> Dr. Gerrit Eichner                   Mathematical Institute, Room 212
> gerrit.eichner using math.uni-giessen.de   Justus-Liebig-University Giessen
> Tel: +49-(0)641-99-32104          Arndtstr. 2, 35392 Giessen, Germany
> http://www.uni-giessen.de/eichner
> ---------------------------------------------------------------------
>
> Am 08.11.2019 um 15:38 schrieb Ana Marija:
> > Hello,
> >
> > I have a data frame like this:
> >
> >> head(dt,20)
> >       chr    pos         gene_id pval_nominal  pval_ret       wl      wr
> >   1: chr1  54490 ENSG00000227232    0.6084950 0.7837780 31.62278 21.2838
> >   2: chr1  58814 ENSG00000227232    0.2952110 0.8975820 31.62278 21.2838
> >   3: chr1  60351 ENSG00000227232    0.4397880 0.8679590 31.62278 21.2838
> >   4: chr1  61920 ENSG00000227232    0.3195280 0.6018090 31.62278 21.2838
> >   5: chr1  63671 ENSG00000227232    0.2377390 0.9880390 31.62278 21.2838
> >   6: chr1  64931 ENSG00000227232    0.2766790 0.9070370 31.62278 21.2838
> >   7: chr1  81587 ENSG00000227232    0.6057930 0.6167630 31.62278 21.2838
> >   8: chr1 115746 ENSG00000227232    0.4078770 0.7799110 31.62278 21.2838
> >   9: chr1 135203 ENSG00000227232    0.4078770 0.9299130 31.62278 21.2838
> > 10: chr1 138593 ENSG00000227232    0.8464560 0.5696060 31.62278 21.2838
> >
> > it is very big,
> >> dim(dt)
> > [1] 73719122        8
> >
> > To count number of unique rows for all 3 columns: chr, pos and gene_id
> > I could just join those 3 columns and than count. But how would I find
> > unique number of rows for these 4 columns without joining them?
> >
> > Thanks
> > Ana
> >
> > ______________________________________________
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> >
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.