Thanks This works a treat & Is exactly what I was looking for Tom On Mon, Feb 11, 2013 at 6:08 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Tom, > > > On 2/11/2013 11:35 AM, Tom Oates wrote: > >> Hi >> I am very much a learner in R in general& GenomicRanges in general >> >> I am struggling to find documentation to help me get my head around >> distanceToNearest in GenomicRanges >> If I have a GRanges object: >> >> GRanges with 6 ranges and 4 metadata columns: >> seqnames ranges strand | >> <rle> <iranges> <rle> | >> [1] 10 [ 96723746, 96723747] - | >> [2] 7 [ 13641170, 13641171] + | >> [3] 16 [ 17772801, 17772802] - | >> [4] 3 [ 88173502, 88173503] - | >> [5] 13 [106979682, 106979683] + | >> [6] 9 [104393139, 104393140] + | >> >> (You will notice that all the regions are only dinucleotides& I have >> >> removed the metadata ) >> >> I have a 2nd GRanges object which is ensembl rat transcripts as below: >> 39549 ranges and 2 metadata columns: >> seqnames ranges strand | tx_id >> tx_name >> <rle> <iranges> <rle> |<integer> >> <character> >> [1] 1 [5473, 16844] + | 1 >> ENSRNOT00000044270 >> [2] 1 [5526, 16968] + | 2 >> ENSRNOT00000049921 >> [3] 1 [5526, 16968] + | 3 >> ENSRNOT00000051735 >> [4] 1 [5598, 13520] + | 4 >> ENSRNOT00000034630 >> [5] 1 [8268, 16850] + | 5 >> ENSRNOT00000044505 >> [6] 1 [8316, 17577] + | 6 >> ENSRNOT00000042693 >> [7] 1 [8884, 16850] + | 7 >> ENSRNOT00000044187 >> [8] 1 [8956, 9955] + | 8 >> ENSRNOT00000041082 >> [9] 1 [9055, 17351] + | 9 >> ENSRNOT00000050254 >> >> >> If I invoke: >> xx<-distanceToNearest(diff.**cpgs.gr <http: diff.cpgs.gr="">, >> rat.transcripts, ignore.strand=F) >> >> xx >> DataFrame with 1133 rows and 3 columns >> queryHits subjectHits distance >> <integer> <integer> <integer> >> 1 1 7752 0 >> 2 2 32166 11946 >> 3 3 14678 25377 >> 4 4 24286 66747 >> 5 5 10609 34242 >> 6 6 37076 122683 >> 7 7 35184 0 >> 8 8 34180 45561 >> 9 9 19351 50156 >> ... ... ... ... >> etc >> >> I am uncertain how I would then use the xx output to gain information >> (i.e. >> tx_id, tx_name) about the feature which the function has identified as >> nearest? >> I would be happy to supply any more info as required >> > > The subjectHits column gives the row of your transcript GRanges object > that matches the corresponding query row. I am assuming here that the ' > diff.cpgs.gr' GRanges object is longer than 6? Anyway, here is an example > using your data and the TxDb.Mmusculus.UCSC.mm10.**knownGene package: > > > > x > GRanges with 6 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr10 [ 96723746, 96723747] * > [2] chr7 [ 13641170, 13641171] * > [3] chr16 [ 17772801, 17772802] * > [4] chr3 [ 88173502, 88173503] * > [5] chr13 [106979682, 106979683] * > [6] chr9 [104393139, 104393140] * > --- > > y <- transcripts(TxDb.Mmusculus.**UCSC.mm10.knownGene) > > xx <- distanceToNearest(x, y, ignore.strand=F) > > xx > DataFrame with 6 rows and 3 columns > > queryHits subjectHits distance > <integer> <integer> <integer> > 1 1 4514 100935 > 2 2 45653 0 > 3 3 19383 0 > 4 4 34197 0 > 5 5 14383 0 > 6 6 54212 8108 > > > > y[xx[,2],] > GRanges with 6 ranges and 2 metadata columns: > > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] chr10 [ 96617001, 96622811] + | 33419 uc007gww.2 > [2] chr7 [ 13623967, 13670807] + | 21400 uc012ezp.1 > [3] chr16 [ 17759663, 17779206] + | 48288 uc007ylz.1 > [4] chr3 [ 88171560, 88177785] - | 10107 uc008puf.2 > [5] chr13 [106963757, 107022114] - | 43288 uc007rue.1 > [6] chr9 [104361832, 104385031] + | 29956 uc009rhp.1 > --- > seqlengths: > chr1 chr2 ... chrUn_JH584304 > 195471971 182113224 ... 114452 > > Best, > > Jim > > > Tom >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]