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]