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getGeneSets: Prepare Pathway Data for the MLP Function

Description Usage Arguments Value Examples

Description

The return value of the getGeneSets function has as primary use to serve as geneSet argument for the MLP function

Usage

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getGeneSets(species = "Mouse", geneSetSource = NULL, entrezIdentifiers)

Arguments

species

character vector of length one indicating the species, one of 'Mouse', 'Human' or 'Rat'; defaults to 'Mouse'.

geneSetSource

source to be used to construct the list of pathway categories; for public data sources, the user can specify a string (one of 'GOBP', 'GOMF', 'GOCC', 'KEGG' or 'REACTOME') and BioC packages will be used to construct the list of pathway categories; for non-public data sources, the user can pass the pathway data as a dataframe with (at least) the following four columns: PATHWAYID, TAXID, PATHWAYNAME and GENEID. It is assumed all columns are of type character.

entrezIdentifiers

Entrez Gene identifiers used to subset the relevant gene set

Value

object of class geneSetMLP which is essentially a named list of pathway categories. Each list component contains a vector of Entrez Gene identifiers related to that particular pathway

Examples

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if (require(GO.db) && require(org.Mm.eg.db)){
  pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
  pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
  load(pathExampleData)
  load(pathExamplePValues)
  geneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = names(examplePValues)[1:2000])
  head(geneSet)
}


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