Question: Ensembl biomaRt down
gravatar for sergio.artsc
14 months ago by
sergio.artsc0 wrote:

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="")

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.

When I go to the URL, the server status is down.

Thank you very much.

biomart ensembl • 522 views
ADD COMMENTlink modified 14 months ago by genomax71k • written 14 months ago by sergio.artsc0
gravatar for genomax
14 months ago by
United States
genomax71k wrote:

Must have been a temporary glitch. It is up now.

> snp_db <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="")
> 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
ADD COMMENTlink written 14 months ago by genomax71k
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