Martin Morgan wrote: > Hi Andrew -- > > I guess the thread you reference is about finding entrez ids when > chromosome locations are known, whereas you're doing something > different. I don't think the end positions are in the org.Hs.eg > packages. > > One strategy is to use biomaRt, e.g., > > >> library(biomaRt) >> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") >> getGene(c("1", "100"), listFilters(mart)[59, 1], mart=mart) >> > entrezgene hgnc_symbol > 1 1 A1BG > 2 100 ADA > description > 1 Alpha-1B-glycoprotein precursor (Alpha-1-B glycoprotein). [Source:Uniprot/SWISSPROT;Acc:P04217] > 2 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase). [Source:Uniprot/SWISSPROT;Acc:P00813] > chromosome_name band strand start_position end_position ensembl_gene_id > 1 19 q13.43 -1 63548356 63556669 ENSG00000121410 > 2 20 q13.12 -1 42681578 42713795 ENSG00000196839 > > Martin > > > "Andrew Yee" <yee at="" post.harvard.edu=""> writes: > > >> I've been exploring the org.Hs.eg package. I can see how you can get start >> locations of genes from org.Hs.egCHRLOC, but how do you get the end location >> for a given gene ID? Apologies if this is obvious. I've already looked >> through the info here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2007-December/020625.html >> >> and don't see this explicitly addressed. >> >> Thanks, >> Andrew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Hi Andrew, AFAIK none of the annotation packages has ever had the "end positions" available. I am still searching for more information about why we have this tradition although I think it may be just because we have always provided annotations that are more gene centric rather than more transcript centric. I take it from your request that you would like for this information to be included as well? Marc

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