Using older Annotations in GenomeGraph Library
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@philippe-thomas-3565
Last seen 8.2 years ago
Hi all, I'm currently using the GenomeGraph library to visualise my data. However, I'm currently encountering the following problem: The data I want to visualise is from Human Genome Build 36.3. I'm also loading gene annotation information using makeGeneRegion, which itself imports data from ensembl. My problem of course is, that my own data is generated on Build 36.3 and the genome annotation is based on Build 37.1. So my first idea was to use a older version of biomart, by: mart <- useMart("ensembl_mart_49", archive=TRUE, dataset= "hsapiens_gene_ensembl") This is not working, as I get the error message: Invalid attribute(s): ensembl_exon_id Does anybody have any other ideas to solve this problem? Or maybe someone knows how to generate my own annotation information? Any help would be appreciated, Philippe
Annotation biomaRt Annotation biomaRt • 645 views
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@steffenstatberkeleyedu-2907
Last seen 8.2 years ago
Hi Philippe, You can connect to Ensembl 54 which is ncbi36 by: mart = useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org", dataset="hsapiens_gene_ensembl") That should give you the annotation you want. Cheers, Steffen > Hi all, > > I'm currently using the GenomeGraph library to visualise my data. > However, I'm currently encountering the following problem: > > The data I want to visualise is from Human Genome Build 36.3. I'm also > loading gene annotation information using makeGeneRegion, which itself > imports data from ensembl. My problem of course is, that my own data is > generated on Build 36.3 and the genome annotation is based on Build 37.1. > > So my first idea was to use a older version of biomart, by: > mart <- useMart("ensembl_mart_49", archive=TRUE, dataset= > "hsapiens_gene_ensembl") > > This is not working, as I get the error message: > Invalid attribute(s): ensembl_exon_id > > Does anybody have any other ideas to solve this problem? Or maybe > someone knows how to generate my own annotation information? > > Any help would be appreciated, > > Philippe > > _______________________________________________ > 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 >
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