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.eich...@math.uni-giessen.de Justus-Liebig-University Giessen
Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany
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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.eich...@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.eich...@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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