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

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

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 (Bgee release 13.2 and before) "fpkm" for RNA-seq (Bgee release 14 and above) "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")
  dataMouseGSE43721 <- getData(bgee, experimentId = "GSE43721")
  dataMouseGSE43721.fpkm <- formatData(bgee,
                                       dataMouseGSE43721,
                                       callType = "present",
                                       stats = "fpkm")
}

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