Question: biomaRt: Cannot access the zebra fish dataset
0
gravatar for francois
15 months ago by
francois10
francois10 wrote:

I cannot access the zebra fish ensembl database with biomaRt in R...

# biomaRt
library (biomaRt)

listMarts()

ensembl <- useMart("ensembl")

listDatasets(ensembl) #output is really bad, with huge spaces between lines (cannot copy it here)

listDatasets(ensembl)$dataset

Can't see the zebra fish dataset in the list!

ensembl = useDataset("drerio_gene_ensembl", mart = ensembl)

That returns:

Error in useDataset("drerio_gene_ensembl", mart = ensembl) : 
  The given dataset:  drerio_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

While it looks like the correct name (I'm following a tutorial)... What is happening?

biomart R • 640 views
ADD COMMENTlink modified 15 months ago by Mike Smith1.1k • written 15 months ago by francois10
5
gravatar for Mike Smith
15 months ago by
Mike Smith1.1k
EMBL Heidelberg / de.NBI
Mike Smith1.1k wrote:

There was an issue with one of the new primate datasets having an apostrophe in its description, which was causing listDatasets() to fail. I have patched this in version 2.35.1 and pushed it to the Bioconductor devel branch. This will take a few days to propagate, so the fastest way to get hold if it is via Github using

BiocInstaller::biocLite('grimbough/biomaRt')

If people could report back if that works or not that would be very helpful, and assuming it works I will also patch the release version of biomaRt.

> library(biomaRt)
> packageVersion("biomaRt")
[1] ‘2.35.1’

> ensembl_mart <- useMart("ensembl")
> dim( listDatasets(ensembl_mart) )
[1] 97  3
ADD COMMENTlink written 15 months ago by Mike Smith1.1k

Amazing, that works beautifully. I was stuck with 46 datasets for whatever reason, now I have all 97 available. Thanks Mike!

ADD REPLYlink written 15 months ago by francois10
1
gravatar for Sej Modha
15 months ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

This is reported on the support forum of the bioconductor by other users too. A workaround is also presented there: https://support.bioconductor.org/p/104025/

ADD COMMENTlink modified 15 months ago • written 15 months ago by Sej Modha4.1k
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