I am trying to access the Ensembl Regulatory Build through the biomaRt package, using the following commands:
ensembl_mart <- biomaRt::useMart(“ENSEMBL_MART_FUNCGEN") ensembl_mart <- biomaRt::useDataset(“hsapiens_regulatory_feature", mart = ensembl_mart) queryAttributes <- c('regulatory_stable_id','feature_type_description','feature_type_name') ensembl_reg <- biomaRt::getBM(attributes = queryAttributes, mart=ensembl_mart) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
I do not believe the availability of the web service is the underlying problem here. I have tried both GRCh38 and GRCh37, but neither was successful.
Does anyone know how/if Ensembl's regulatory data can be obtained through biomaRt?
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
attached base packages:
 stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
 IRanges_2.6.0 rsconnect_0.4.3 parallel_3.3.0 DBI_0.4-1 tools_3.3.0 RCurl_1.95-4.8 Biobase_2.32.0 AnnotationDbi_1.34.3 biomaRt_2.28.0 RSQLite_1.0.0
 S4Vectors_0.10.1 BiocGenerics_0.18.0 stats4_3.3.0 bitops_1.0-6 XML_3.98-1.4