Question: biomaRt: Cannot access the zebra fish dataset
0
gravatar for francois
21 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 • 817 views
ADD COMMENTlink modified 4 days ago by fatimarasool13540 • written 21 months ago by francois10

Hi Mike Smith, I am using the biomart package. and i have not seen dataset of wheat. Can you please tell me how to acess the wheat dataset ?

ADD REPLYlink written 4 days ago by fatimarasool13540

I would recommend you start a new topic with this question since it is unlikely to be the same issue as reported here, and include some details of the code you have already tried.

ADD REPLYlink written 4 days ago by Mike Smith1.3k
5
gravatar for Mike Smith
21 months ago by
Mike Smith1.3k
EMBL Heidelberg / de.NBI
Mike Smith1.3k 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 21 months ago by Mike Smith1.3k

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

ADD REPLYlink written 21 months ago by francois10
1
gravatar for Sej Modha
21 months ago by
Sej Modha4.4k
Glasgow, UK
Sej Modha4.4k 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 21 months ago • written 21 months ago by Sej Modha4.4k
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