geo_download function

geo_download

download gse data and get informations

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

Returns

a list with exp,pd and gpl

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)

See Also

find_anno

Author(s)

Xiaojie Sun