[R] how to find number of unique rows for combination of r columns
Bert Gunter
bgunter@4567 @end|ng |rom gm@||@com
Fri Nov 8 16:59:29 CET 2019
Sorry, but you ask basic questions.You really need to spend some more time
with an R tutorial or two. This list is not meant to replace your own
learning efforts.
You also do not seem to be reading the docs carefully. Under ?unique, it
links ?duplicated and tells you that it gives indices of duplicated rows of
a data frame. These then can be used by subscripting to remove those rows
from the data frame. Here is a reproducible example:
df <- data.frame(a = 1:3, b = letters[c(1,1,2)], d = LETTERS[c(1,1,2)])
df[-duplicated(df[,2:3]), ] ## Note the - sign
If you prefer, the "Tidyverse" world has what are purported to be more
user-friendly versions of such data handling functionality that you can use
instead.
Bert
On Fri, Nov 8, 2019 at 7:38 AM 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.
>
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