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

Boris Steipe bor|@@@te|pe @end|ng |rom utoronto@c@
Fri Nov 8 17:49:44 CET 2019 

Good. Duplicated returns a boolean index vector that you can use to extract the non-unique rows. 

B.



> On 2019-11-08, at 11:30, Ana Marija <sokovic.anamarija using gmail.com> wrote:
> 
> I am trying to first identify how many duplicate rows are there determined by the unique values in the first 3 columns. Now I know that is about 20000 rows which are non unique. But I would like to extract all 8 columns for those non unique rows and see what is going on with META value I have in them. 
> 
> About duplicated() function I know as well as about unique
> 
> On Fri, 8 Nov 2019 at 10:08, Boris Steipe <boris.steipe using utoronto.ca> wrote:
> Are you trying to eliminate duplicated rows from your dataframe? Because that would be better achieved with duplicated().
> 
> 
> B.
> 
> 
> 
> 
> > On 2019-11-08, at 10:32, Ana Marija <sokovic.anamarija using gmail.com> wrote:
> > 
> > would you know how would I extract from my original data frame, just
> > these unique rows?
> > because this gives me only those 3 columns, and I want all columns
> > from the original data frame
> > 
> >> head(udt)
> >   chr   pos         gene_id
> > 1 chr1 54490 ENSG00000227232
> > 2 chr1 58814 ENSG00000227232
> > 3 chr1 60351 ENSG00000227232
> > 4 chr1 61920 ENSG00000227232
> > 5 chr1 63671 ENSG00000227232
> > 6 chr1 64931 ENSG00000227232
> > 
> >> head(dt)
> >    chr   pos         gene_id pval_nominal pval_ret       wl      wr      META
> > 1: chr1 54490 ENSG00000227232     0.608495 0.783778 31.62278 21.2838 0.7475480
> > 2: chr1 58814 ENSG00000227232     0.295211 0.897582 31.62278 21.2838 0.6031214
> > 3: chr1 60351 ENSG00000227232     0.439788 0.867959 31.62278 21.2838 0.6907182
> > 4: chr1 61920 ENSG00000227232     0.319528 0.601809 31.62278 21.2838 0.4032200
> > 5: chr1 63671 ENSG00000227232     0.237739 0.988039 31.62278 21.2838 0.7482519
> > 6: chr1 64931 ENSG00000227232     0.276679 0.907037 31.62278 21.2838 0.5974800
> > 
> > On Fri, Nov 8, 2019 at 9:30 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >> 
> >> Thank you so much! Converting it to data frame resolved the issue!
> >> 
> >> On Fri, Nov 8, 2019 at 9:19 AM Gerrit Eichner
> >> <gerrit.eichner using math.uni-giessen.de> wrote:
> >>> 
> >>> It seems as if dt is not a (base R) data frame but a
> >>> data table. I assume, you will have to transform dt
> >>> into a data frame (maybe with as.data.frame) to be
> >>> able to apply unique in the suggested way. However,
> >>> I am not familiar with data tables. Perhaps somebody
> >>> else can provide a more profound guess.
> >>> 
> >>>  Regards  --  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 16:02 schrieb 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
> >>>>>> 
> >>>>>> ______________________________________________
> >>>>>> 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.
> >>>>>> 
> >>>>> 
> >>>>> ______________________________________________
> >>>>> 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.
> > 
> > ______________________________________________
> > 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.
> 
> ______________________________________________
> 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.

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