venn {limma} | R Documentation

## Venn Diagrams

### Description

Compute classification counts or plot classification counts in a Venn diagram.

### Usage

    vennCounts(classification, include="both")
    vennDiagram(object, include="both", names, ...)

### Arguments

`classification` | classification matrix of 0's and 1's indicating significance of a test. Usually created by `classifyTests`.
`object` | either a classification matrix or a `VennCounts` object produced by `vennCounts`.
`include` | character string specifying whether to counts genes up-regulated, down-regulated or both. Choices are `"both"`, `"up"` or `"down"`.
`names` | optional character vector giving names for the sets or contrasts
`...` | any other arguments are passed to `plot`

### Value

`vennCounts` produces a `VennCounts` object, which is a numeric matrix with last column `"Counts"` giving counts for each possible vector outcome.

### Author(s)

Gordon Smyth and James Wettenhall

### See Also

An overview of linear model functions in limma is given by 5.LinearModels.

### Examples

    tstat <- matrix(rt(300,df=10),100,3)
    tstat[1:33,] <- tstat[1:33,]+2
    clas <- classifyTests(tstat,df=10,p.value=0.05)
    a <- vennCounts(clas)
    print(a)
    vennDiagram(a)

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