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

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

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 documentation built on Nov. 8, 2020, 8:21 p.m.