In my case, looks like never end. I need to check my R first.
Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 12/20/13 12:05 PM, "Hervé Pagès" <hpa...@fhcrc.org> wrote: >Hi Jianhong, > >According to my timings, it's a little bit slower than exonsBy() but >not that much. It has to do a little bit more work too as the introns >are not explicitly stored in the SQLite db (the exons are) but are >inferred from the exons and transcript boundaries. >So intronsByTranscript() has to retrieve all the exons + all the >transcripts from the db. > >intronsByTranscript(): > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > system.time(introns <- >intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 9.165 0.076 9.263 > system.time(introns <- >intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 4.824 0.064 4.896 > >exonsBy(): > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > system.time(exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 7.720 0.072 7.812 > system.time(exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 4.229 0.028 4.265 > >transcripts(): > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > system.time(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 1.424 0.008 1.436 > system.time(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)) > # user system elapsed > # 0.776 0.012 0.790 > >Less than 10 sec. to retrieve all the exons and transcripts from disk >and compute the 659327 introns. It's actually not that bad. > >Cheers, >H. > > >On 12/20/2013 08:25 AM, Ou, Jianhong wrote: >> Dear all, >> >> When I try to use intronsByTranscript to get introns for hg19 known >>genes, I found it is unacceptable slow. Does any body has the same >>problem? >> >> My code: >> library(GenomicFeatures) >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> introns <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene) >> >>> sessionInfo() >> R Under development (unstable) (2013-12-12 r64453) >> Platform: x86_64-apple-darwin12.5.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.15.4 >> [3] AnnotationDbi_1.25.9 Biobase_2.23.3 >> [5] GenomicRanges_1.15.15 XVector_0.3.5 >> [7] IRanges_1.21.17 BiocGenerics_0.9.2 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.19.1 Biostrings_2.31.5 bitops_1.0-6 >> BSgenome_1.31.7 >> [5] DBI_0.2-7 GenomicAlignments_0.99.9 RCurl_1.95-4.1 >> Rsamtools_1.15.15 >> [9] RSQLite_0.11.4 rtracklayer_1.23.6 stats4_3.1.0 >> tools_3.1.0 >> [13] XML_3.98-1.1 zlibbioc_1.9.0 >> >> Yours sincerely, >> >> Jianhong Ou >> >> LRB 670A >> Program in Gene Function and Expression >> 364 Plantation Street Worcester, >> MA 01605 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >-- >Hervé Pagès > >Program in Computational Biology >Division of Public Health Sciences >Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N, M1-B514 >P.O. Box 19024 >Seattle, WA 98109-1024 > >E-mail: hpa...@fhcrc.org >Phone: (206) 667-5791 >Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
