Hi Hervé Thank you for the detailed instructions! They do help. Best, ZQ On Fri, Jan 3, 2014 at 6:33 AM, Hervé Pagès <hpages@fhcrc.org> wrote: > Hi ZQ, > > > On 01/01/2014 12:51 AM, Zhi-Qiang Ye wrote: > >> Hi, thanks for your help. >> >> The information I need is the 'rn4' coordinates of Entrez Genes, so I >> finally used the 'refGene' table and 'refLink' table downloaded from UCSC >> genome browser database under the directory of 'rn4', and got what I need. >> > > Following Steve's original suggestion (but using the refGene table > instead of ensGene): > > library(GenomicFeatures) > txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='refGene') > gn <- genes(txdb) > > This gives you the 'rn4' coordinates of Entrez Genes: > > > head(gn) > GRanges with 6 ranges and 1 metadata column: > seqnames ranges strand | gene_id > <rle> <iranges> <rle> | <characterlist> > 100034253 chrX [ 40301219, 40334396] - | 100034253 > 100036582 chr8 [ 18755584, 18756808] + | 100036582 > 100036765 chr12 [ 32898194, 32924599] + | 100036765 > 100049583 chr8 [114071508, 114072510] - | 100049583 > 100124593 chr8 [128569564, 128570618] + | 100124593 > 100125361 chr10 [ 45764849, 45775258] - | 100125361 > --- > seqlengths: > chr1 chr2 chr3 ... chrUn chrUn_random > 267910886 258207540 171063335 ... 75822765 6862066 > > > head(as.character(mcols(gn)$gene_id)) > [1] "100034253" "100036582" "100036765" "100049583" "100124593" > "100125361" > > Note that makeTranscriptDbFromUCSC() downloads and uses the 'refGene' > and 'refLink' tables from UCSC for you in order to generate the > TranscriptDb object 'txdb'. In addition to being convenient, this > method also avoids some of the common pitfalls of downloading and > processing those tables "manually". > > Cheers, > H. > > > As for other information not related to the chromosomal locations, I just >> used the information in the package 'org.Rn.eg.db'. >> >> Maybe the maintainner can still provide official packages based on 'rn4', >> say, 'org.Rn4.eg.db', since annotation based on 'rn5' is not as complete >> as >> that based on 'rn4'. >> >> Best, >> ZQ >> >> On Sat, Dec 21, 2013 at 8:53 AM, Marc Carlson <mcarlson@fhcrc.org> wrote: >> >> Steve is right. You could go and do that. However in this case we have >>> already done the work for you. You can find a package here: >>> >>> http://www.bioconductor.org/packages/release/data/annotation/html/ TxDb. >>> Rnorvegicus.UCSC.rn4.ensGene.html >>> >>> That should get you transcript locations for RN4. >>> >>> For more information about how you can make use of that resource and of >>> others like it, please be sure to also peak at our workflow: >>> >>> http://www.bioconductor.org/help/workflows/annotation/annotation/ >>> >>> >>> Marc >>> >>> >>> >>> >>> >>> On 12/18/2013 10:09 PM, Steve Lianoglou wrote: >>> >>> Hi, >>>> >>>> On Wed, Dec 18, 2013 at 6:20 PM, Zhi-Qiang Ye <yezhiqiang@gmail.com> >>>> wrote: >>>> >>>> Hi, all >>>>> >>>>> I need to analysis genes whose chromosomal locations are >>>>> based >>>>> on >>>>> the rat genome version rn4, so installed 'org.Rn.eg.db'. However, the >>>>> genome coordinate system is based on rn5. >>>>> >>>>> Is there any way to get and install old versions of >>>>> 'org.Rn.eg.db'? >>>>> >>>>> You might consider building a TranscriptDb object from rn4 annotations >>>> using the GenomicFeatures package: >>>> >>>> http://bioconductor.org/packages/release/bioc/html/GenomicFeature s.html >>>> >>>> Read through its vignette to figure out how to download and build a >>>> TranscriptDb from UCSC. It's going to be something like: >>>> >>>> R> library(GenomicFeatures) >>>> R> txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='ensGene') >>>> >>>> Keep reading to figure out how to lookup genes/transcripts by >>>> (ensembl) transcript IDs, and I think you should be good to go. >>>> >>>> If you need to do sequence related analyses using these annotations, >>>> you can use the rn4 BSgenome object, to boot: >>>> >>>> http://bioconductor.org/packages/release/data/annotation/html/BSg enome. >>>> Rnorvegicus.UCSC.rn4.html >>>> >>>> HTH, >>>> -steve >>>> >>>> >>>> _______________________________________________ >>> 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 >>> >>> >> [[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 >> >> > -- > 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: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]