Thank you for your reply Paul. I had only read the vignette and should have read also the reference manual. That said it is still not working. The example: gr <- GRanges("chr1", IRanges(rep(10, 3), width=6), c("+", "-", "*")) gr promoters(gr, 2, 2) Gives and error: Error: could not find function "promoters" I've updated the GenomicRanges to 1.10.0 (sessionInfo bellow). Also from what I've read in the reference manual, "promoter" will return the region around the TSS: "The return object is a GRanges of promoter regions around the transcription start site the span of which is defined by upstream and downstream. Ranges on the * strand are treated the same as those on the + strand.", something like upstream.TSS.downstream (very similar to the function flank), whereas I am interested in extending the range to something like upstream+FullGene. Please correct me if I am wrong. On another note, did the behaviour of transcriptsBy(hg19RefGenes, by='gene') changed in the last update? I thought the output was GRanges object but now it is a GRangesList. Best regards, António On 29 October 2012 13:55, Paul Shannon <pshannon@fhcrc.org> wrote: > Hi Antonio, > > New methods in Genomic Features 1.10.0 > > promoter > getPromoterSeq > > might help you out here. The latter uses the former, and a documented > example can be found here: > > > http://www.bioconductor.org/help/workflows/gene-regulation-tfbs /#compact-summary > > If this is insufficient please let us know, and we can dig further into > your problem. > > Cheers, > > - Paul > > -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]

Thanks for your suggestions Michael, On 29 October 2012 14:35, Michael Lawrence <lawrence.michael@gene.com>wrote: > > On Mon, Oct 29, 2012 at 3:37 AM, António Miguel de Jesus Domingues < > amjdomingues@gmail.com> wrote: > >> Hi Bioconducters, >> >> I have a GRanges object created with the package GenomicFeatures that >> contains gene coordinates: >> >> ########################################################## >> hg19RefGenes <- loadFeatures(file='hg19RefGenes.sqlite') >> hg19RefGenes >> >> # generate a GRanges object containing contiguous transcribed regions of >> the genome (from the 1st to last exon) >> GeneRegions <- transcriptsBy(hg19RefGenes, by='gene') >> gene.bounds <- seqapply(GeneRegions, range, progress="text") >> > > You should be able to simply call range() on GeneRegions, i.e., no need to > call seqapply. Btw, what is the progress="text" argument here? I'm not > aware of this feature. > In this case I actually have a GRangesList and it does not work. I was doing one too many things and posted the result after seqapply/unlist and not the TranscriptbBy. Ah, the progress=text is not a feature as far as I'm aware (and it does not work). I was experimenting with something else and got in the mail somehow. > > >> GeneRegions <- unlist(gene.bounds) >> head(GeneRegions) >> GRanges with 6 ranges and 0 elementMetadata cols: >> seqnames ranges strand >> <rle> <iranges> <rle> >> 1 chr19 [ 58858172, 58864865] - >> 10 chr8 [ 18248755, 18258723] + >> 100 chr20 [ 43248163, 43280376] - >> 1000 chr18 [ 25530930, 25757445] - >> 10000 chr1 [243651535, 244006886] - >> 100008586 chrX [ 49217771, 49342266] + >> --- >> seqlengths: >> chr1 chr2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >> ########################################################## >> >> I want to do something that should be simple: extend the ranges to that it >> also includes 1Kb upstream of the gene (~Promoter region), for example, >> chr19 [ 58858172, 58864865] becomes chr19 [ 58858172, 58865865]. Looking >> at the GenomicFeatures fucntions it seems that neither resize or flank >> will >> do. Is there another function that I am missing that will do the job ? >> >> > resize() should work. Simply call resize(GeneRegions, width(GeneRegions) + > 1000L, fix = "end"). > > This tip is great - it works beautifully! Cheers. > Michael > > >> Cheers, >> António >> >> -- >> -- >> António Miguel de Jesus Domingues, PhD >> Neugebauer group >> Max Planck Institute of Molecular Cell Biology and Genetics, Dresden >> Pfotenhauerstrasse 108 >> 01307 Dresden >> Germany >> >> e-mail: domingue@mpi-cbg.de >> tel. +49 351 210 2481 >> The Unbearable Lightness of Molecular Biology >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> 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 >> > > -- -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]