hi Valerie, That's great, thanks. After the next release, I will change the parathyroidSE vignette to use disjointExons() and the new arguments for summarizeOverlaps(): 1. use inter.feature=FALSE for the exon counting rather than the custom counting mode 2. use fragments=TRUE rather than counting pairs and singletons separately best, Mike On Mon, Jul 1, 2013 at 10:20 AM, Alejandro Reyes <alejandro.reyes at="" embl.de=""> wrote: > Thanks Valerie! > > I will make sure to change all the documentation to use "disjointExons" > instead. > > Best regards, > Alejandro > > > >> Mike and Alejandro, >> >> disjointExons() is now in GenomicFeatures 1.13.18. It's documented on the >> same man page as ?transcripts, ?exons, ?cds ,etc. >> >> The function is the same as DEXSeq::prepareAnnotationForDEXSeq with a few >> performance modifications. Primary changes were a helper function with a >> more vectorized approach to create 'geneNames', 'transcripts' and reducing >> the number of times metadata columns were added to the GRanges. >> >> > txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene >> > system.time(prepareAnnotationForDEXSeq(txdb, TRUE, TRUE)) >> user system elapsed >> 8.205 0.028 8.397 >> > system.time(disjointExons(txdb, TRUE, TRUE)) >> user system elapsed >> 5.596 0.032 5.764 >> >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> > system.time(prepareAnnotationForDEXSeq(txdb, TRUE, TRUE)) >> user system elapsed >> 37.286 0.228 37.954 >> > system.time(disjointExons(txdb, TRUE, TRUE)) >> user system elapsed >> 28.130 0.228 28.822 >> >> The multiple requests on the mailing list for a function of this type made >> me think it should be included in one of the infrastructure packages. The >> goal of adding this to GenomicFeatures was to increase visibility and make >> it more readily available to packages that don't depend on DEXSeq. I hope >> having the function in two places doesn't add a layer of confusion. I have a >> suite of unit tests to ensure disjointExons and prepareAnnotationForDEXSeq >> are in sync. >> >> Let me know if you have any questions or would like any changes made to >> the man page. >> >> Thanks, >> Valerie >> >> >> >> On 06/11/13 12:30, Valerie Obenchain wrote: >>> >>> Great. I'll go ahead and put this in GenomicFeatures with credit to you >>> and Alejandro. >>> >>> Thanks. >>> Valerie >>> >>> On 06/11/2013 09:39 AM, Michael Love wrote: >>>> >>>> hi Valerie, >>>> >>>> On Tue, Jun 11, 2013 at 6:13 PM, Valerie Obenchain >>>> <vobencha at="" fhcrc.org=""> wrote: >>>>> >>>>> Hi Mike (Love), >>>>> >>>>> Would you be interested in contributing a disjointExons() to >>>>> GenomicFeatures? I think this extraction would be useful to many. >>>>> Maybe we >>>>> also want a disjointExonsBy() but the only 'by' would be genes ...? >>>>> >>>>> Valerie >>>>> >>>> >>>> I'd be happy to contribute any of this code in parathyroidSE. >>>> Alejandro Reyes has formalized this part of the code into the >>>> following function in DEXSeq >= 1.6.0: >>>> >>>>> prepareAnnotationForDEXSeq >>>> >>>> function (transcriptDb, aggregateGenes = FALSE, includeTranscripts = >>>> TRUE) >>>> { >>>> stopifnot(is(transcriptDb, "TranscriptDb")) >>>> exonsByGene <- exonsBy(transcriptDb, by = "gene") >>>> exonicParts <- disjoin(unlist(exonsByGene)) >>>> if (!aggregateGenes) { >>>> overlaps <- findOverlaps(exonicParts, exonsByGene) >>>> geneNames <- names(exonsByGene)[subjectHits(overlaps)] >>>> ..... >>>> >>>> best, >>>> >>>> Mike >>>> >>> >>> _______________________________________________ >>> 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 >> >> >