compendiumdb (version 1.0.3)

loadDataToCompendium: Load GSE into the compendium database

Description

Load the data from SOFT files corresponding to the specified GSE and GPL(s) into the tables of the MySQL compendium database

Usage

loadDataToCompendium(con, GSEid, GPLid = "", datadir = getwd())

Arguments

con

list containing a connection object specifying the user name and password to connect or interact with the compendium database (see connectDatabase)

GSEid

character string specifying the GSE ID to be loaded into the

compendium database

GPLid

character vector specifying the GPL ID(s). The default value is "" and will load all the GPL ID(s) corresponding to the GSE specified by GSEid.

datadir

directory where the BigMac directory used for storing the SOFT files downloaded from GEO has been created (see downloadGEOdata). The default directory is the current working directory.

Details

The SOFT files downloaded from GEO using the function downloadGEOdata are parsed and loaded into the compendium database. This function can be called once all the SOFT files corresponding to the specified GSEid have been downloaded to the BigMac directory (see downloadGEOdata). The BigMac directory should be a subdirectory of the directory specified by the user via the argument datadir. The GPLid argument provides the option to only load the data for a specific platform.

See Also

downloadGEOdata

Examples

 ## Not run: 
#   conn <- connectDatabase(user="usrname",password="passwd",dbname="compendium")
#   downloadGEOdata("GSE1657")
# 
#   # GSE1657 has GPL96 and GPL97 platform data. Load only GPL96 data
#   loadDataToCompendium(conn,"GSE1657","GPL96")
# 
#   # Load both GPL96 and GPL97 as a character vector
#   loadDataToCompendium(conn,"GSE1657",c("GPL96","GPL97"))
#   # Both platforms can also be loaded using the default value for GPLid
# 
#   # Load multiple GSEs to the compendium
#   for (i in  c("GSE4251","GSE6495","GSE12597","GSE1657")){
#    loadDataToCompendium(con=conn,GSEid=i)
#   }
#  ## End(Not run)