downloadAndProcessGEO: Download GEO dataset and preprocess it

In AEBilgrau/DLBCLdata: Automated and reproducible download and preprocessing of DLBCL data

Description

Functionality for automatically downloading, RMA preprocessing the array data and formatting the phenotype data, and saving the results in a .Rds file.

Usage

downloadAndProcessGEO(geo_nbr, destdir = getwd(), ..., clean = FALSE,
  verbose = TRUE)

Arguments

geo_nbr	The GEO ascession number.
destdir	The destination dir of the downloaded files.
...	Arguments passed to preprocessCELFiles
clean	Should the strictly unnessesary files be deleted?
verbose	Signal the process.

Value

Creates a folder with the downloaded and processed files. The processed files are saved as an .Rds object named after the used parameters. Invisibly returns the saved object.

Note

The function will overwrite existing files in the destdir.

Arguments after ... must be named.

Author(s)

Anders Ellern Bilgrau, Steffen Falgreen Larsen

Examples

## Not run: 
print(DLBCL_overview)
geo_nbr <- DLBCL_overview[6,1]
res <- downloadAndProcessGEO(geo_nbr = geo_nbr, cdf = "brainarray",
                             target = "ENSG", clean = FALSE)
head(exprs(res$es$Batch1))

## End(Not run)

AEBilgrau/DLBCLdata documentation built on May 5, 2019, 11:29 a.m.