Skip to contents

Open the GEO landing page in a browser

Source: R/geo-.R
geo_show.Rd

Construct a GEO landing page and open it directly in the system's default web browser (or a user-specified browser). By default, this function uses the brief amount of html format data for all entities.

Usage

geo_show(
  accession,
  famount = NULL,
  scope = NULL,
  ftp_over_https = NULL,
  browser = getOption("browser")
)

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.

browser

a non-empty character string giving the name of the program to be used as the HTML browser. It should be in the PATH, or a full path specified. Alternatively, an R function to be called to invoke the browser.

Under Windows NULL is also allowed (and is the default), and implies that the file association mechanism will be used.

Details

See utils::browseURL()

References

Examples

if (interactive()) {
    geo_show("gpl96")
}