downloadAndProcessDLBCL: Download and process all curated DLBCL datasets

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

Description

Automatically download and process all support curated DLBCL datasets. Simply loops over all datasets in data(dlbcl_overview).

Usage

downloadAndProcessDLBCL(...)

Arguments

...	Arguments passed to downloadAndProcessGEO.

Value

Saves a list of the processed datasets in the working directory named "dlbcl_data.Rds". Invisibly returns a list of the output of downloadAndProcessGEO.

Author(s)

Anders Ellern Bilgrau
Steffen Falgreen Larsen

Examples

listTargets("brainarray")
## Not run: 
# Warning, very long processing times if data is not downloaded.

# Preprocess with brainarray "Entrez" gene ids
res <- downloadAndProcessDLBCL(cdf = "brainarray", target = "ENTREZG",
                               clean = FALSE)

# Preprocess with brainarray "Ensembl" gene ids
res2 <- downloadAndProcessDLBCL(cdf = "brainarray", target = "ENSG",
                                clean = TRUE)

# Preprocess with affy's probesets
res3 <- downloadAndProcessDLBCL()  #= downloadAndProcessDLBCL(cdf = "affy")

## End(Not run)

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