Get the metadata of multiple GEO identities

This function is useful for combining with geo_search() to filter results, as geo_search() cannot retrieve the full metadata for all GEO identifiers. By default, this function uses the soft format for GDS and GSE entities, and the full amount of text format data for GPL and GSM entities.

Usage

geo_meta(
  accession,
  famount = NULL,
  scope = NULL,
  ftp_over_https = NULL,
  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.

famount

A character specifying either:

the file format on the GEO FTP server, or
the amount of data in the GEO Accession Display Bar.

See geo_url() for details on the format and amount arguments.

scope

A character specifying which GEO accessions to include (Only applicable to Accession Display Bar access).

"none": Applicable only to DataSets; for DataSets, this is also the sole valid option
"self": the queried accession only.
"gsm", "gpl", "gse": related samples, platforms, or series.
"all": all accessions related to the query (family view).

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 data frame contains metadata of all ids.

Examples

# \donttest{
geo_meta("GSE10", odir = tempdir())
#> Found 1 file already downloaded
#>                   Database_name Database_institute
#> 1 Gene Expression Omnibus (GEO)       NCBI NLM NIH
#>                 Database_web_link       Database_email Series_title
#> 1 http://www.ncbi.nlm.nih.gov/geo geo@ncbi.nlm.nih.gov     eye-SAGE
#>   Series_geo_accession         Series_status Series_submission_date
#> 1                GSE10 Public on Oct 03 2001            Oct 03 2001
#>   Series_last_update_date Series_pubmed_id
#> 1             Apr 18 2012         11756676
#>                                                                                                                                                                                                                Series_summary
#> 1 Human retinal and RPE SAGE libraries.; Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).; Keywords: other
#>                    Series_type
#> 1 Expression profiling by SAGE
#>                                                   Series_contributor
#> 1 Dror,,Sharon; Seth,,Blackshaw; Constance,L,Cepko; Thaddeus,P,Dryja
#>                 Series_sample_id Series_contact_name
#> 1 GSM571; GSM572; GSM573; GSM574        Dror,,Sharon
#>           Series_contact_email Series_contact_phone Series_contact_fax
#> 1 dror_sharon@meei.harvard.edu         617-573-4347       617-573-3168
#>              Series_contact_laboratory Series_contact_department
#> 1 Ocular Molecular Genetics Laboratory                          
#>    Series_contact_institute Series_contact_address Series_contact_city
#> 1 Massachusetts Eye and Ear        243 Charles St.              Boston
#>   Series_contact_state Series_contact_zip/postal_code Series_contact_country
#> 1                   MA                          02114                    USA
#>            Series_contact_web_link Series_platform_id Series_platform_taxid
#> 1 http://eyegene.meei.harvard.edu/               GPL4                  9606
#>   Series_sample_taxid
#> 1                9606
#>                                                  Series_relation
#> 1 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA84465
# }