listBgeeSpecies: List species in the Bgee database and the available data...

In BgeeDB/BgeeDB_R: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

List species in the Bgee database and the available data types for each of them

Description

Returns information on available species in Bgee

Usage

listBgeeSpecies(
  release = NULL,
  ordering = NULL,
  allReleases = NULL,
  removeFile = TRUE
)

Arguments

release	A character specifying a targeted release number. In the form "Release.subrelease" or "Release_subrelease", e.g., "13.2" or 13_2". If not specified, the latest release is used.
ordering	A numeric indicating the number of the column which should be used to sort the data frame. Default NULL, returning unsorted data frame.
allReleases	A data frame with information on all releases. Avoid redownloading this information if .getBgeeRelease() already called.
removeFile	Boolean indicating whether the downloaded file should be deleted. Default to TRUE.

Value

A data frame with species Id, genus name, species name, common name and data type availability for targeted Bgee release

Author(s)

Julien Roux

Examples

{
 listBgeeSpecies()
 # species present in a specific Bgee release
 listBgeeSpecies(release = "13.2")
 # in order to order species according to theit taxonomical IDs
 listBgeeSpecies(ordering = 1)
}

BgeeDB/BgeeDB_R documentation built on Jan. 14, 2024, 4:29 a.m.