can you get end position information from org.Hs.eg
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Andrew Yee ▴ 350
@andrew-yee-2667
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@martin-morgan-1513
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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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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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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Marc Carlson wrote: > 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 > > _______________________________________________ > 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 again Andrew, Another thing that I always seem to forget about are the CHRLOC packages. And for some reason in my head I never think of these CHRLOC packages as part of the set of things that are considered "annotation packages" either (I guess because they are so specialized). But in your case you can just use the humanCHRLOC package, and that would get you all kinds of information about the end points for these genes. Marc
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