compendiumdb (version 1.0.3)

downloadGEOdata: Download a GSE record from GEO

Description

Downloads the SOFT files for the GSE, GPLs, GSMs, and GDSs corresponding to the GSE identifier provided by the user from GEO to the user's local machine

Usage

downloadGEOdata(GSEid, destdir = getwd())

Arguments

GSEid

character string specifying the GSE to be downloaded from GEO

destdir

directory where to locate the BigMac directory used for storing the SOFT files downloaded from GEO. The default directory is the current working directory

Details

In the Gene Expression Omnibus (GEO) high-throughput functional genomics data is stored in SOFT (Simple Omnibus Format in Text) file format. Examples are the series record (GSE), the sample record (GSM), the platform record (GPL), and the dataset record (GDS). More information about the different types of SOFT files can be found at http://www.ncbi.nlm.nih.gov/geo/info/overview.html. The function downloadGEOdata uses (or creates, if it does not exist yet) a data directory called BigMac in a directory destdir specified by the user. The BigMac directory contains several subdirectories: annotation, COMPENDIUM, data and log. The data directory contains further subdirectories to store the downloaded .soft files corresponding to GSEs, GSMs, GPLs, and GDSs downloaded from GEO. More information about the structure of the BigMac directory can be found at http://wiki.bioinformaticslaboratory.nl/foswiki/bin/view/BioLab/CompendiumDB. If an existing BigMac directory is detected that already contains the necessary SOFT files, these files will not be downloaded from GEO again.

See Also

loadDatabaseSchema, loadDataToCompendium

Examples

 ## Not run: 
#   # Download the files related to the specified GSE from GEO to the BigMac directory 
#   # in the user's current working directory
#   downloadGEOdata(GSEid="GSE23183")
#  ## End(Not run)