getAnnotation: Retrieve Bgee experiments annotation for targeted species and...

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

Retrieve Bgee experiments annotation for targeted species and data type.

Description

This function loads the annotation of experiments and samples of quantitative expression datasets (rna_seq, affymetrix, sc_full_length) that are available from Bgee.

Usage

getAnnotation(myBgeeObject)

Arguments

myBgeeObject

A Reference Class Bgee object, notably specifying the targeted species and data type.

Value

A list of two elements, including a data frame of the annotation of experiments for chosen species (field "experiment.annotation") and a data frame of the annotation of chips/libraries from these experiments (field "sample.annotation").

Author(s)

Andrea Komljenovic and Julien Roux.

Examples

{
  bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
  myAnnotation <- getAnnotation(bgee)
}

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