Thanks Hervé! 2016-10-17 2:18 GMT-05:00 Hervé Pagès <hpa...@fredhutch.org>:
> Hi Shilin, > > I answered this on the support site: > > https://support.bioconductor.org/p/88232/#88347 > > Cheers, > H. > > > On 10/16/2016 08:35 PM, zhao shilin wrote: > >> Dear BioC team, >> >> I think I found something incorrect in TxDb.Hsapiens.UCSC.hg38.knownG >> ene, >> and reported in https://support.bioconductor.org/p/88232/ but didn't get >> reply. I think it is a bug, so decided to send it via email to let you >> know. >> >> I am using the developing version of TxDb.Hsapiens.UCSC.hg38.knownGene, >> because the release version is build in 2015 and has a lot of difference >> with UCSC website. Here is the R code for the bug: >> >> require(TxDb.Hsapiens.UCSC.hg38.knownGene) >> require(GenomicRanges) >> >> geneDb=TxDb.Hsapiens.UCSC.hg38.knownGene >> allGeneRange<-genes(geneDb) >> allGeneRange["875"] >> txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg38.knownGene) >> txs["875"] >> >> >> We can find CBS gene (txs["875"]) has 25 transcripts, from two >> regions: chr21 [6444869, 6467509] and chr21 [43075107, 43076288] >> >> 1. CBS gene ("875") was only in chr21 [43075107, 43076288]. The region >> of chr21 [6444869, 6467509] was CBSL gene ("102724560"). But CBSL was >> not >> in the database, and its transcripts were recorded in CBS. >> >> 2. The gene region of CBS gene (allGeneRange["875"]) was in chr21 >> [6444869, >> 43076943], which included all the region between 6444869-43076943. But it >> is not correct as they were two separate regions. >> >> >> Thanks! >> >> Shilin >> >> [[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...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel