getES: Load ExpressionSet by GEO identifier

In phantasus: Visual and interactive gene expression analysis

Description

getES return the ExpressionSet object(s) corresponding to GEO identifier.

Usage

getES(
  name,
  type = NA,
  destdir = tempdir(),
  mirrorPath = "https://ftp.ncbi.nlm.nih.gov"
)

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.
type	Type of the dataset: 'GSE' or 'GDS'. If not specified, the function will take first three letters of name variable as type.
destdir	Directory for caching loaded Series and GPL files from GEO database.
mirrorPath	URL string which specifies the source of matrices.

Value

List of ExpressionSet objects, that were available by given in name variable GEO identifier.

Examples

## Not run: 
    getES('GSE14308', type = 'GSE', destdir = 'cache')
    getES('GSE27112')

## End(Not run)
getES('GDS4922')

phantasus documentation built on Nov. 8, 2020, 6:39 p.m.