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methylUser
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10
@methyluser-5943
Last seen 9.5 years ago
Hello, I've been trying to connect to biomart for several times and I am not managing. Does anyone know a solution to this please?
Below is the code I am using to connect:
library("biomaRt")
ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "feb2014.archive.ensembl.org", verbose=TRUE)
ensembl = useDataset("hsapiens_gene_ensembl", mart=ensembl, verbose=TRUE)
filt = c("chromosome_name", "start", "end")
val = list(chromosome_name='10', start_position='6205875', end_position='6205875')
att = c("ensembl_gene_id", "external_gene_id", "gene_biotype", "chromosome_name", "start_position", "end_position")
getBM(attributes=att, filters=filt, values=val, mart=ensembl, verbose=TRUE)
Error given:
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.

This is likely C: Problem with biomart's listMarts function and it's not in our hands -- I have contacted the ensembl help desk.