makeDB {FunctSNP} | R Documentation |
Build a species-specific database from external sources using dbAutoMaker - a suite of Perl scripts to download data from public databases (e.g. NCBI) and build an SQLite database. Note that Perl MUST be installed and the computer has to be connected to the internet. For further details on dbAutoMaker visit http://www.csiro.au/science/dbAutoMaker.html
makeDB(speciesCode, db.list=FALSE)
speciesCode |
A vector containing 3 letter species codes[Default = the species code set by setSpecies ()] |
db.list |
TRUE or FALSE [Default = FALSE] |
Use the argument db.list=TRUE to display the species codes for databases that can be made.
The function is called for its side-effect. It builds a new species-specific database and saves it in the FunctSNP library.
The species added to FunctSNP by using addSpecies
are not supported by makeDB (). Use userAddedSpecies
to list user added species.
S. J. Goodswen <Stephen.Goodswen@csiro.au>
http://www.csiro.au/science/FunctSNP.html http://www.csiro.au/science/dbAutoMaker.html
# list databases that can be made makeDB(db.list=TRUE) ## Not run: # Build database for Bos_taurus makeDB("bta") # Build the databases for Gallus gallus and Sus scrofu species <- c("gga","ssc") makeDB(species) # Build default species database set by setSpecies() makeDB() ## End(Not run)