getInfo: Download raw expression data from GEO DataSet

In gibbslab/coexnet: coexnet: An R package to build CO-EXpression NETworks from Microarray Data

Description

Using a GSE ID list, from the GEO DataSets FTP, it searches and downloads each raw expression data in a separate file with the GSE ID as the name. After, the function uncompresses the downloaded file to be ready to use. Additionally, searches and downloaded the information of the chip using the GPL ID to obtain the .soft file.

Usage

getInfo(GSE, GPL, directory = ".")

Arguments

GSE	The list of GSE ID.
GPL	The GPL ID of the chip used in the microarray experiment.
directory	The path file to download and uncompress the raw expression data, by default is the current path file.

Value

A set of files with the uncompressed data and ready to use.

Author(s)

Juan David Henao <[e-mail]>

See Also

getAffy to charge the expression data.

Examples

## Not run: 
# Extract data from GEO DataSets (Takes time)

getInfo(GSE = "GSE8216", GPL = "GPL2025",directory = tempdir())

## End(Not run)

gibbslab/coexnet documentation built on May 17, 2019, 4:19 a.m.