I couldn't find the externalgeneid attribute in the new biomaRt version.
Is there any reason for that?
Thanks a lot.
Which dataset are you trying to use? I'm not sure there has ever been an external_gene_id attribute for hsapiens (at least not looking at archives back for the past few years), do you mean to use external_gene_name?
You can search for the available attributes with searchAttributes() e.g to look in the October 2016 archive you can use
mart <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensembl', version = "86")
searchAttributes(mart = mart, "external_gene")
I'm using :
ensembl <- useMart(biomart = "plants_mart",
dataset = "athaliana_eg_gene",
host = "plants.ensembl.org")
features <- getBM(attributes = c("ensembl_gene_id",
filters = c("ensembl_gene_id"),
mart = ensembl)
Ensembl Plants has fewer archives than the main Ensembl site (I only know of http://oct2017-plants.ensembl.org ) so it's harder to check if things have changed, but I don't see an external_gene_id there either:
> ensembl <- useMart(biomart = "plants_mart",
+ dataset = "athaliana_eg_gene",
+ host = "http://oct2017-plants.ensembl.org")
> searchAttributes(ensembl, "external")
name description page
15 external_gene_name Gene name feature_page
16 external_gene_source Source of gene name feature_page
142 external_gene_name Gene name structure
143 external_gene_source Source of gene name structure
173 external_gene_name Gene name homologs
174 external_gene_source Source of gene name homologs
904 external_gene_name Gene name snp
905 external_gene_source Source of gene name snp
950 external_gene_name Gene name sequences
951 external_gene_source Source of gene name sequences
Of course it could have been introduced and then removed again between then and now.
I should have mentioned in my previous post that this isn't something that the biomaRt package has introduced. It only allows you to access whatever data and options Ensembl make available. If something has changed or been removed then you probably want to contact the Ensembl helpdesk for an explanation (http://ensemblgenomes.org/info/about/contact ).
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