On 04/19/2013 08:45 AM, Valerie Obenchain wrote: > Hello, > > query <- GRanges("chr1", IRanges(c(5, 20), width=1)) > subject <- GRanges("chr1", IRanges(c(30, 10, 1), width=1, > names=c("gene1", "gene2"))) > out <- precede(query, subject) > > out > [1] 3 1 > > You can add metdata columns to a GRanges with 'mcols<-'. This assignment will > replace any existing metadata columns with 'subjectNames'. > mcols(query) <- DataFrame(subjectNames=names(subject)[out]) > > If you want to keep the existing metadata columns, use append() on the right side: > mcols(query) <- append(mcols(query), > DataFrame(subjectNames=names(subject)[out])) or just query$subjectNames = names(subject)[out] > > > > Valerie > > > On 04/19/2013 07:27 AM, Tom Oates wrote: >> Dear All >> I have GRanges objects of transcript information (subject) & for regions of >> interest (query). >> Top lines of (subject): >> 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 >> >> Top lines of (query): >> seqnames ranges strand >> <rle> <iranges> <rle> >> [1] 10 [ 37958164, 37958165] + | >> [2] 7 [ 46598224, 46598225] - | >> [3] 1 [ 9627018, 9627019] - | >> [4] 9 [ 10158183, 10158184] + | >> [5] 2 [185436985, 185436986] + | >> [6] 8 [ 93638247, 93638248] - | >> [7] 7 [ 68559015, 68559016] - | >> [8] 12 [ 10978744, 10978745] + | >> [9] 17 [ 33460790, 33460791] - | >> >> and am using the precede command to find the preceeding transcripts to my >> regions of interest >> >> output<-precede(query, subject, ignore.strand=FALSE) >> >> I am aware that the object called "output" is of class integer with the row >> names of "subject" which represent the preceding hits for "query", but I >> have so far been unable to use these row names to end up with a granges >> object with the name of the preceding transcripts as metadata in a granges >> object containing the ranges from "query" i.e something that would look >> like: >> [1] 10 [ 37958164, 37958165] + |ENSRNOT00000044270 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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