Ensembl biomaRt down
I am trying to get some queries from biomaRt package. I am defining the next connection:
snp_db <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="grch37.ensembl.org")
and I get the following message:
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
When I go to the URL, the server status is down.
Thank you very much.
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1 answer
Must have been a temporary glitch. It is up now.
> snp_db <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="grch37.ensembl.org")
> getBM(attributes = c('refsnp_id','allele','chrom_start','chrom_strand'),
+ filters = c('chr_name','start','end'),
+ values = list(8,148350,148612),
+ mart = snp_db)
refsnp_id allele chrom_start chrom_strand
1 rs546813474 C/T 148402 1
2 rs201635470 A/C 148556 1
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