biomaRt: Cannot access the zebra fish dataset
2
0
Entering edit mode
6.8 years ago
francois ▴ 80

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 • 3.6k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
5
Entering edit mode
6.8 years ago
Mike Smith ★ 2.1k

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 COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
6.8 years ago
Sej Modha 5.3k

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 COMMENT

Login before adding your answer.

Traffic: 876 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6