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

Description Usage Arguments Value Author(s) Examples

View source: R/formatData.R

Description

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

Usage

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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

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{
  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.