Currently db_ucsc and db_ensembl are available for connections.

db_ucsc(dbname, host = "genome-mysql.cse.ucsc.edu", user = "genomep",
  password = "password", port = 3306, ...)

db_ensembl(dbname, host = "ensembldb.ensembl.org", user = "anonymous",
  password = "", port = 3306, ...)

Arguments

dbname

name of database

host

hostname

user

username

password

password

port

MySQL connection port

...

params for connection

See also

Examples

# NOT RUN {
if(require(RMySQL)) {
  ucsc <- db_ucsc('hg38')

  # fetch the `refGene` tbl
  tbl(ucsc, "refGene")

  # the `chromInfo` tbls have size information
  tbl(ucsc, "chromInfo")
}
# }
# NOT RUN { if(require(RMySQL)) { # squirrel genome ensembl <- db_ensembl('spermophilus_tridecemlineatus_core_67_2') tbl(ensembl, "gene") } # }