GEOmetadb (version 1.32.2)

getBiocPlatformMap: Get mappings between GPL and Bioconductor microarry annotation packages

Description

Query the gpl table and get GPL information of a given list of Bioconductor microarry annotation packages. Note currently the GEOmetadb does not contains all the mappings, but we are trying to construct a relative complete list.

Usage

getBiocPlatformMap(con, bioc='all')

Arguments

con

Connection to the GEOmetadb.sqlite database

bioc

Character vector of Biocondoctor microarry annotation packages, e.g. c('hgu133plus2','hgu95av2'). 'all' returns all mappings.

Value

A six-column data.frame including GPL title, GPL accession, bioc_package, manufacturer, organism, data_row_count.

References

http://meltzerlab.nci.nih.gov/apps/geo

Examples

if(file.exists('GEOmetadb.sqlite')) {
    con <- dbConnect(SQLite(), "GEOmetadb.sqlite")
	getBiocPlatformMap(con)[1:5,]
	getBiocPlatformMap(con, bioc=c('hgu133a','hgu95av2'))
	dbDisconnect(con)
} else {
  print("You will need to usethe getSQLiteFile() function to get a copy
of the SQLite database file before this example will work")
}