formatData: Format RNA-seq or Affymetrix data downloaded from Bgee.

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

Format RNA-seq or Affymetrix data downloaded from Bgee.

Description

This function formats the data downloaded with the getData() function into an object of the Bioconductor "expressionSet" Class.

Usage

formatData(myBgeeObject, data, stats = NULL, callType = "all")

Arguments

myBgeeObject	A Reference Class Bgee object, notably specifying the targeted species and data type.
data	A list of data frames including data from multiple experiments, or a data frame including data from a single experiment.
stats	A character indicating what expression values should be used in the formatted data expressionSet object matrix. "rpkm" for RNA-seq "counts" for RNA-seq "tpm" for RNA-seq (Bgee release 14 and above) "intensities" for Affymetrix microarrays
callType	A character indicating whether intensities should be displayed only for present (i.e., expressed) genes, present high quality genes, or all genes (default). "present" "present high quality" "all"

Value

If data was a list of data frames from multiple experiments, returns a list of ExpressionSet objects. If data was a data frame from a single experiment, returns an ExpressionSet object.

Author(s)

Andrea Komljenovic and Julien Roux.

Examples

{
  bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
  dataMouseGSE30617 <- getData(bgee, experimentId = "GSE30617")
  dataMouseGSE30617.rpkm <- formatData(bgee, dataMouseGSE30617, callType = "present", stats = "rpkm")
}

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