getGeneSets {MLP} | R Documentation

## Prepare Pathway Data for the MLP Function

### Description

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

### Usage

    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 is named with the pathway ID and contains a vector of Entrez Gene identifiers related to that particular pathway.
The object contains additionally the attributes:

- 'species' and 'geneSetSource': `species` and `geneSetSource` (as provided as input)

- 'descriptions': named character vector with pathway descriptions. The vector is named with the pathway ID.

### Examples

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

[Package MLP version 1.40.0 Index]