get_geo_suppl: Get Supplemental Files from GEO

In Yunuuuu/rgeo: R interface for GEO database

Get Supplemental Files from GEO

Description

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 by the computer.

Usage

get_geo_suppl(
  ids,
  dest_dir = getwd(),
  pattern = NULL,
  ftp_over_https = TRUE,
  handle_opts = list(connecttimeout = 60L)
)

Arguments

ids	A character vector representing the GEO entity for downloading and parsing. All ids must in the same GEO identity (c("GDS505", "GDS606") are all GEO DataSets, c("GSE2", "GSE22") are all GEO series eg.).
dest_dir	The destination directory for any downloads. Defaults to current working dir.
pattern	character string containing a regular expression to be matched in the supplementary file names.
ftp_over_https	A scalar logical value indicates whether to connect GEO FTP site with https traffic. If TRUE, will download FTP files from https://ftp.ncbi.nlm.nih.gov/geo, which is used by GEOquery, otherwise, will use ftp://ftp.ncbi.nlm.nih.gov/geo directly.
handle_opts	A list of named options / headers to be set in the handle.

Value

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

Examples

a <- get_geo_suppl("GSM1137", tempdir())
a

Yunuuuu/rgeo documentation built on Dec. 23, 2024, 10:01 p.m.