geo_download: geo_download

In tinyarray: Expression Data Analysis and Visualization

geo_download

Description

Download GEO expression data and return the expression matrix, phenotype data, and platform information.

Usage

geo_download(
  gse,
  by_annopbrobe = TRUE,
  simpd = TRUE,
  colon_remove = TRUE,
  download_timeout = getOption("timeout"),
  destdir = getwd(),
  n = 1
)

Arguments

gse	GEO accession number or a path to a cached '.rds' or '.RData' file containing an 'ExpressionSet' or a list of 'ExpressionSet' objects
by_annopbrobe	whether to try the AnnoProbe cache first and fall back to GEOquery::getGEO()
simpd	whether to simplify phenotype data by dropping columns with a single unique value
colon_remove	whether to drop raw 'characteristics_ch1*' columns while keeping the derived ':ch1' phenotype column names intact
download_timeout	timeout in seconds used for GEOquery fallback and for mirror stall detection during the resumable download
destdir	The destination directory for data downloads
n	For data with more than one ExpressionSet, specify which one to analyze

Details

Cached 'eSet' objects are stored as '.rds' files in 'destdir'; legacy '.Rdata' cache files are still readable, and incomplete cache files will be kept so the download can resume automatically.

Value

a list with 'exp', 'pd', 'gpl', and 'group_candidates', or 'NULL' when the data cannot be read or downloaded

Author(s)

Xiaojie Sun

See Also

find_anno

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
}

## End(Not run)

tinyarray documentation built on Aug. 2, 2026, 9:07 a.m.