tinyarray (version 3.0.0)

geo_download: 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
)

Value

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

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

Author

Xiaojie Sun

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.

See Also

find_anno

Examples

if (FALSE) {
if(requireNamespace("Biobase",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
}
}