downloadGEOdata: Download a GSE record from GEO
In compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

Description Usage Arguments Details Note Author(s) See Also Examples

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

1	downloadGEOdata(GSEid, destdir = getwd())

`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

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.

If the BigMac directory already exists, the function downloadGEOdata will try to store the downloaded data in the existing directory structure. Therefore, in order to avoid errors, do not change BigMac's directory structure.

Umesh K. Nandal

loadDatabaseSchema, loadDataToCompendium

 ## 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)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

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    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: RMySQL
Loading required package: DBI
sh: 1: perl: Permission denied