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
character string specifying the GSE to be downloaded from GEO
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.
downloadGEOdata uses (or creates, if it does not
exist yet) a data directory called
BigMac in a directory
destdir specified by the user.
BigMac directory contains several subdirectories:
data directory contains further subdirectories to store
.soft files corresponding to GSEs, GSMs, GPLs,
and GDSs downloaded from GEO. More information about the structure of
BigMac directory can be found at
If an existing BigMac directory is detected that already contains the necessary
SOFT files, these files will not be downloaded from GEO again.
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
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## 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)