R: Plot overlap of gene sets and core set

plotOverrepresentation {GiANT} | R Documentation

## Plot overlap of gene sets and core set

### Description

Plots a Venn diagramm of the overlaps of the core set and gene sets in an overrepresentation analysis.

### Usage

    plotOverrepresentation(
    	object,
    	signLevel = object$signLevel,
    	subset = NULL,
    	aggregate = FALSE,
    	ask = FALSE,
    	...)

### Arguments

`object` | A result of a call to `geneSetAnalysis` using the predefined analysis `analysis.customOverrepresentation` or `analysis.overrepresentation`.
`signLevel` | Only results with significance level smaller than the given value are included in the venn diagram.
`subset` | Indices for the results that should be included in the diagram.
`aggregate` | Specifies whether all gene sets should be plotted in a single Venn diagram (which is possible for at most four gene sets) or whether there should be one Venn diagram for each gene set.
`ask` | If set to true, the plot function will prompt for a user input for each new plot that is shown on an interactive device (see `par("ask")`). If `aggregate = TRUE`, `ask` is ignored.
`...` | Further parameters to be passed to `vennDiagram`.

### See Also

`geneSetAnalysis`, `predefinedAnalyses`, `gsAnalysis`

### Examples

    # load data
    require(GlobalAncova)
    data(vantVeer)
    data(phenodata)
    data(pathways)

    # use the absolute correlation as a gene-level statistic
    stat <- abs(apply(vantVeer,1,cor,y = phenodata$metastases))
    # define the core set as the 25% genes with the highest correlation
    coreSet <- rownames(vantVeer)[tail(order(stat), 25)]

    # perform an overrepresentation analysis
    resOverrep <- geneSetAnalysis(
    	dat = vantVeer,
    	geneSets = pathways,
    	analysis = analysis.customOverrepresentation(),
    	coreSet = coreSet,
    	adjustmentMethod = "fdr")

    # plot a Venn diagram
    plotOverrepresentation(resOverrep, subset = 1:3, aggregate = TRUE)

[Package GiANT version 1.2 Index]