[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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