geo_download: geo_download

In tinyarray: Expression Data Analysis and Visualization

geo_download

Description

download gse data and get informations

Usage

geo_download(
  gse,
  by_annopbrobe = TRUE,
  simpd = TRUE,
  colon_remove = FALSE,
  destdir = getwd(),
  n = 1
)

Arguments

gse	gse assession number
by_annopbrobe	download data by geoquery or annoprobe
simpd	get simplified pdata,drop out columns with all same values
colon_remove	whether to remove duplicated columns with colons
destdir	The destination directory for data downloads.
n	For data with more than one ExpressionSet, specify which one to analyze

Value

a list with exp,pd and gpl

Author(s)

Xiaojie Sun

See Also

find_anno

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    print("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')"print)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    print("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')"print)
  }
}

## End(Not run)

tinyarray documentation built on June 22, 2024, 9:58 a.m.