Hello, Is there any way to add rownames to an IRanges object? What I am trying to do is try and make it easy to reference back to the original table that created the IRanges object after an overlap. Hs1plus <- with(HsapiensAnnot[HsapiensAnnot$seqname == "1" & HsapiensAnnot$strand == "+",], IRanges(start, end)) yoda1plus <- with(yip[yip$seqname == "chr1" & yip$strand == "+",], IRanges(start, end)) yoda1plus <- yoda1plus[order(start(yoda1plus)),] seqoverlap <- overlap(Hs1plus,yoda1plus,multiple=F) At the moment to get information about the overlaps I have to do something like: HsapiensAnnot[HsapiensAnnot$start == start(Hs1plus[seqoverlap[1],]) & HsapiensAnnot$seqname=="1",] but I am sure that there is a better way and this can't deal with the NAs that might be in seqoverlap Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

Daniel, IRanges objects do support names and they can be added using the "names<-" replacement function. > suppressMessages(library(IRanges)) > myranges <- IRanges(start = c(1,3,5,7), end = c(2,4,8,9)) > names(myranges) <- c("a", "b", "c", "d") > myranges IRanges object: start end width names 1 1 2 2 a 2 3 4 2 b 3 5 8 4 c 4 7 9 3 d > myranges[c("c", "a", "d", "b")] IRanges object: start end width names 1 5 8 4 c 2 1 2 2 a 3 7 9 3 d 4 3 4 2 b > sessionInfo() R version 2.9.0 Under development (unstable) (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.1.34 loaded via a namespace (and not attached): [1] grid_2.9.0 lattice_0.17-20 Matrix_0.999375-18 Daniel Brewer wrote: > Hello, > > Is there any way to add rownames to an IRanges object? What I am trying > to do is try and make it easy to reference back to the original table > that created the IRanges object after an overlap. > > Hs1plus <- with(HsapiensAnnot[HsapiensAnnot$seqname == "1" & > HsapiensAnnot$strand == "+",], IRanges(start, end)) > > yoda1plus <- with(yip[yip$seqname == "chr1" & yip$strand == "+",], > IRanges(start, end)) > yoda1plus <- yoda1plus[order(start(yoda1plus)),] > > seqoverlap <- overlap(Hs1plus,yoda1plus,multiple=F) > > At the moment to get information about the overlaps I have to do > something like: > HsapiensAnnot[HsapiensAnnot$start == start(Hs1plus[seqoverlap[1],]) & > HsapiensAnnot$seqname=="1",] > > but I am sure that there is a better way and this can't deal with the > NAs that might be in seqoverlap > > Thanks > > Dan >

On Fri, Jan 23, 2009 at 2:30 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > Hello, > > Is there any way to add rownames to an IRanges object? What I am trying > to do is try and make it easy to reference back to the original table > that created the IRanges object after an overlap. > > Hs1plus <- with(HsapiensAnnot[HsapiensAnnot$seqname == "1" & > HsapiensAnnot$strand == "+",], IRanges(start, end)) > > yoda1plus <- with(yip[yip$seqname == "chr1" & yip$strand == "+",], > IRanges(start, end)) > yoda1plus <- yoda1plus[order(start(yoda1plus)),] > > seqoverlap <- overlap(Hs1plus,yoda1plus,multiple=F) > > At the moment to get information about the overlaps I have to do > something like: > HsapiensAnnot[HsapiensAnnot$start == start(Hs1plus[seqoverlap[1],]) & > HsapiensAnnot$seqname=="1",] > > but I am sure that there is a better way and this can't deal with the > NAs that might be in seqoverlap > Patrick answered the names question, but I'd also like to suggest using RangedData here. It looks like you're getting your data from a GFF file. With rtracklayer, you could import() this directly into a RangedData. This would make things a fair bit easier: yoda1plus <- ranges(yip[strand(yip) == "+",]) ans <- HsapiensAnnot[strand(HsapiensAnnot) == "+",][yoda1plus] 'ans' would contain the RangedData with the annotations on the positive strand, that overlap with the IRanges yoda1plus, across all chromosomes. Couple of caveats: - the chromosomes should be named the same between the two datasets (eg of the form chr1). - the ranges in yip should have been sorted - requires development versions of IRanges and rtracklayer Michael > Thanks > > Dan > -- > ************************************************************** > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > Email: daniel.brewer@icr.ac.uk > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. 534147 > with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the...{{dropped:13}}