makeDB {FunctSNP}R Documentation

Build a species-specific database from external sources

Description

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

Usage

makeDB(speciesCode, db.list=FALSE) 

Arguments

speciesCode A vector containing 3 letter species codes[Default = the species code set by setSpecies ()]
db.list TRUE or FALSE [Default = FALSE]

Details

Use the argument db.list=TRUE to display the species codes for databases that can be made.

Value

The function is called for its side-effect. It builds a new species-specific database and saves it in the FunctSNP library.

Note

The species added to FunctSNP by using addSpecies are not supported by makeDB (). Use userAddedSpecies to list user added species.

Author(s)

S. J. Goodswen <Stephen.Goodswen@csiro.au>

References

http://www.csiro.au/science/FunctSNP.html
http://www.csiro.au/science/dbAutoMaker.html

See Also

setSpecies addSpecies

Examples

# 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)


[Package FunctSNP version 1.0-1 Index]