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Question: using ensembl archive in GenomicRanges
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gravatar for anupam sinha
6.4 years ago by
anupam sinha270
anupam sinha270 wrote:
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
ADD COMMENTlink modified 6.4 years ago by Paul Leo970 • written 6.4 years ago by anupam sinha270
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gravatar for Paul Leo
6.4 years ago by
Paul Leo970
Paul Leo970 wrote:
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",dat aset="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@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 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.4 years ago by Paul Leo970
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