Question: BiomaRt and archival versions of ensembl_mart
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gravatar for Greg Slodkowicz
5.7 years ago by
Greg Slodkowicz50 wrote:
Hi, I've been trying to use biomaRt to access a previous release of Ensembl (63) but listMarts(archive=T) reveals only ensembl_mart versions 43-47. Has the support for archival versions of Ensembl been discontinued? I'm using R v. 3.0.1 and biomaRt 2.16.0. Best, Greg -- Greg Slodkowicz PhD student, Nick Goldman group European Bioinformatics Institute (EMBL-EBI) [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.7 years ago by Steffen Durinck540 • written 5.7 years ago by Greg Slodkowicz50
Answer: BiomaRt and archival versions of ensembl_mart
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gravatar for Steffen Durinck
5.7 years ago by
Steffen Durinck540 wrote:
Hi Greg, A better way to access an ensembl archive is to specify the archive URL in the host parameter like this: ensembl=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl" ,host=" jan2013.archive.ensembl.org") This will connect you to Ensembl 70 for example. To figure out which host URL to use for a specific archive version I usually go to www.ensembl.org, select my species of interest and then at the bottom of the page click on "view in archive site" then select the Ensembl version of the archive you want to use and see where the URL points to and use part of the URL before the first forward slash (e.g. jan2013.archive.ensembl.org) as host URL in your useMart call. Best, Steffen On Thu, Aug 29, 2013 at 6:13 AM, Greg Slodkowicz <gregs@ebi.ac.uk> wrote: > Hi, > I've been trying to use biomaRt to access a previous release of Ensembl > (63) but listMarts(archive=T) reveals only ensembl_mart versions 43-47. > Has the support for archival versions of Ensembl been discontinued? I'm > using R v. 3.0.1 and biomaRt 2.16.0. > > Best, > Greg > > > -- > Greg Slodkowicz > PhD student, Nick Goldman group > European Bioinformatics Institute (EMBL-EBI) > > [[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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.7 years ago by Steffen Durinck540
> A better way to access an ensembl archive is to specify the archive URL in > the host parameter like this: > > > ensembl=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensemb l",host=" > jan2013.archive.ensembl.org") > Thanks, that's exactly what I was after. Best, Greg -- Greg Slodkowicz PhD student, Nick Goldman group European Bioinformatics Institute (EMBL-EBI) [[alternative HTML version deleted]]
ADD REPLYlink written 5.7 years ago by Greg Slodkowicz50
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