Description Usage Arguments See Also Examples
View source: R/plotOverrepresentation.R
Plots a Venn diagramm of the overlaps of the core set and gene sets in an overrepresentation analysis.
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object |
A result of a call to |
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 |
... |
Further parameters to be passed to |
geneSetAnalysis
, predefinedAnalyses
, gsAnalysis
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | # 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)
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