Get Supplemental Files from GEO — geo

NCBI GEO allows supplemental files to be attached to GEO Series (GSE), GEO platforms (GPL), and GEO samples (GSM). This function 'knows' how to get these files based on the GEO accession. No parsing of the downloaded files is attempted, since the file format is not generally knowable.

Usage

geo_suppl(
  accession,
  pattern = NULL,
  ftp_over_https = TRUE,
  handle_opts = list(),
  odir = getwd()
)

Arguments

accession

A character of GEO accession IDs. Examples:

DataSets (GDS): "GDS505", "GDS606", "GDS1234", "GDS9999", etc.
Series (GSE): "GSE2", "GSE22", "GSE100", "GSE2000", etc.
Platforms (GPL): "GPL96", "GPL570", "GPL10558", etc.
Samples (GSM): "GSM12345", "GSM67890", "GSM112233", etc.

pattern

character string containing a regular expression to be matched in the supplementary file names.

ftp_over_https

Logical scalar. If TRUE, connects to GEO FTP server via HTTPS (https://ftp.ncbi.nlm.nih.gov/geo); otherwise uses plain FTP (ftp://ftp.ncbi.nlm.nih.gov/geo). Only applicable to GEO FTP server access.

handle_opts

A list of named options / headers to be set in the multi_download.

odir

Destination directory for downloads. Defaults to the current working directory.

Value

A list (or a character atomic verctor if only one accession is provided) of the full file paths of the resulting downloaded files.

Examples

# \donttest{
geo_suppl("GSM1137", odir = tempdir())
#> Downloading 1 file
#> [1] "/tmp/Rtmpe7BWTN/GSM1137.CEL.gz"
# }