addGeneSetDescription {MLP} | R Documentation

## Utility function which adds the biological description of the gene sets as a column to the return value of the MLP function (data frame)

### Description

Utility function which adds the biological description of the gene sets as a column to the return value of the MLP function (data frame)

### Usage

    addGeneSetDescription(object, geneSetSource = NULL)

### Arguments

`object` | object of class 'MLP' as produced by the 'MLP' function
`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. The 'geneSetSource' argument should be the same as the argument provided to the getGeneSets function; defaults to NULL

### Value

the data frame as returned by MLP enriched with an additional column geneSetDescription, providing a concise description of the gene set

### See Also

MLP

### Examples

    if (require(GO.db)){
      pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
      load(pathExamplePValues)
    	 geneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = names(examplePValues))
      mlpResult <- MLP(geneSet = geneSet, geneStatistic = examplePValues, addGeneSetDescription = FALSE)
      head(mlpResult)
      mlpResultsWithGSDescr <- addGeneSetDescription(object = mlpResult, geneSetSource = "GOBP")
      head(mlpResultsWithGSDescr)
    }

[Package MLP version 1.40.0 Index]