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, ...)
dbname | name of database |
---|---|
host | hostname |
user | username |
password | password |
port | MySQL connection port |
... | params for connection |
# 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") } # }