Thank you! Works perfectly! I did not know about the split function -Ninni On Mon, Jan 20, 2014 at 9:03 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 01/20/2014 08:54 AM, Ninni Nahm [guest] wrote: > >> >> Hi all! >> >> I have the following problem. >> >> chr13 1260 1275 chr13_38134720_38136919 >> chr13 1261 1276 chr13_38134720_38136919 >> chr15 839 854 chr15_63332831_63335030 >> chr15 840 856 chr15_63332831_63335030 >> chr15 837 852 chr15_63332831_63335030 >> chr15 842 857 chr15_63332831_63335030 >> In the 2. and 3. column are positions which I want to combine whenever >> the value in column 4 is the same. For example, I would want: >> >> chr13 1260 1276 chr13_38134720_38136919 >> chr15 837 857 chr15_63332831_63335030 >> Any help is highly appreciated!!! >> > > Hi -- Once you've read in the data > > > df = read.table(stdin()) > 0: chr13 1260 1275 chr13_38134720_38136919 > 1: chr13 1261 1276 chr13_38134720_38136919 > 2: chr15 839 854 chr15_63332831_63335030 > 3: chr15 840 856 chr15_63332831_63335030 > 4: chr15 837 852 chr15_63332831_63335030 > 6: chr15 842 857 chr15_63332831_63335030 > 7: > > > you could use the GenomicRanges package to make a 'GRanges' object with > the chromosome coordinates > > > library(GenomicRanges) > > gr = with(df, GRanges(V1, IRanges(V2, V3))) > > then split gr by the fourth column, reduce() the adjacent ranges within > each group, and (if there is one range per group) unlist to a GRanges. > Optionally, you might wish to coerce back to a data.frame (though it will > often make sense to continue your analysis with GRanges) > > > as.data.frame(unlist(reduce(split(gr, df$V4)))) > seqnames start end width strand > chr13_38134720_38136919 chr13 1260 1276 17 * > chr15_63332831_63335030 chr15 837 857 21 * > > Hope that helps, > > Martin > > >> -- output of sessionInfo(): >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]