getData: Retrieve Bgee RNA-seq or Affymetrix data.

In wirawara/BgeeDB: Annotation and gene expression data retrieval from Bgee database

Retrieve Bgee RNA-seq or Affymetrix data.

Description

This function loads the quantitative expression data and presence calls for samples available from Bgee (rna_seq, affymetrix).

Usage

getData(myBgeeObject, experimentId = NULL)

Arguments

myBgeeObject	A Reference Class Bgee object, notably specifying the targeted species and data type.
experimentId	An ArrayExpress or GEO accession, e.g., GSE30617. Default is NULL: takes all available experiments for targeted species and data type.

Value

If experimentId is not specified, returns a list of data frames with data from all experiments for targeted species and data type. If experimentId is specified, returns a data frame with data from this experiment.

Author(s)

Andrea Komljenovic and Julien Roux.

Examples

{
  bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
  dataMouse <- getData(bgee)
  dataMouseGSE30617 <- getData(bgee, experimentId = "GSE30617")
}

wirawara/BgeeDB documentation built on Feb. 10, 2023, 4:15 a.m.