getGDS: Load ExpressionSet from GEO Datasets

In ctlab/phantasus: Visual and interactive gene expression analysis

Load ExpressionSet from GEO Datasets

Description

getGDS return the ExpressionSet object corresponding to GEO Dataset identifier.

Usage

getGDS(
  name,
  destdir = getPhantasusConf("cache_folders")$geo_path,
  mirrorPath = getPhantasusConf("geo_mirrors")
)

Arguments

name	String, containing GEO identifier of the dataset. It should start with 'GSE' or 'GDS' and can include exact GPL to annotate dataset, separated with dash ('-') from the identifier.
destdir	Directory for caching loaded Series and GPL files from GEO database.
mirrorPath	URL string which specifies the source of matrices.

Value

ExpressionSet object wrapped in list, that was available by given in name variable GEO identifier.

Examples

## Not run: 
   getGDS('GDS4922', destdir = tempdir(), mirrorPath = "https://ftp.ncbi.nlm.nih.gov")

## End(Not run)

ctlab/phantasus documentation built on Oct. 11, 2024, 4:11 p.m.