Get the metadata of multiple GEO identities

This is useful to combine with geo_search() and filter results since geo_search() cannot get all long metadata of GEO identities.

Usage

geo_meta(
  ids,
  amount = NULL,
  ftp_over_https = TRUE,
  handle_opts = list(),
  odir = getwd()
)

ids

Character vector of GEO accession IDs to download and parse. All IDs must belong to the same GEO entity type. Examples:

amount

A character string specifying the amount of data to retrieve. One of "brief", "quick", "data", "full", "soft", or "soft_full":

"brief": shows only the accession's attributes.
"quick": shows the accession's attributes and the first 20 rows of its data table.
"full": shows the accession's attributes and the complete data table. This is the default when ids are not DataSets or Series.
"data": omits the accession's attributes, showing only links to other accessions and the full data table.
"soft": SOFT (Simple Omnibus in Text Format) from GEO FTP site. When ids is DataSets or Series, this is the default.
"soft_full": full SOFT (Simple Omnibus in Text Format) files from GEO FTP site by DataSet (GDS) containging additionally contains up-to-date gene annotation for the DataSet Platform.

For DataSet, "data" and "full" will be mapped to "soft" and "soft_full" respectively.

ftp_over_https

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

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.

A data.table contains metadata of all ids.