[ensembl-dev] R biomaRt : listDatasets issue

rm8 rm8 at sanger.ac.uk
Tue Aug 7 15:58:44 BST 2018


Hi All,
I struggling to connect to ENSEMBL 93 using R biomaRt package. 
listData set returns 68 datasets instead of 98 listed the example page and “hsapiens_gene_ensembl” is not included in the list. 


> library("biomaRt")
> listMarts()

================

$               biomart               version
	1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 93
	2   ENSEMBL_MART_MOUSE      Mouse strains 93
	3     ENSEMBL_MART_SNP  Ensembl Variation 93
	4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 93

>  ensembl=useMart("ensembl")
> dim(listDatasets(ensembl))

> dim(listDatasets(ensembl))
	[1] 68  3
 	

> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")


And when I try to connect using the dataset name I get the following error. 

$ Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

 
Thanks in advance for help and suggestions. 

Mamun
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