[BioC] using ensembl archive in GenomicRanges

[Paul Leo]

Not tried it for makeTranscriptDbFromBiomart but probably works the same
was as biomart which would use :



mart<-useMart("ensembl_mart_51",host="apr2011.archive.ensembl.org",dataset="hsapiens_gene_ensembl",archive=TRUE)


see http://www.ensembl.org/index.html and at the very bottom of the page
the "View in archive site" link to get the version you want

you get the strange mart name "ensembl_mart_51"  using:
listMarts(host="apr2011.archive.ensembl.org",archive=TRUE) .. 

Paul Leo


-----Original Message-----
From: anupam sinha <anupam.contact at gmail.com>
To: bioc <Bioconductor at stat.math.ethz.ch>
Subject: [BioC] using ensembl archive in GenomicRanges
Date: Thu, 12 Jan 2012 17:44:09 +1000

Dear all,
               Is there any way to use the command

makeTranscriptDbFromBiomart
(biomart="ensembl",dataset="hsapiens_gene_ensembl",transcript_ids=NULL)

from GenomicRanges package of the Biocunductor so that it can retrieve
data from Ensembl release version  62 instead of the current release
version 65. Thanks in advance for any help.



Anupam

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