VENNset-class {systemPipeR} | R Documentation

## Class `"VENNset"`

### Description

Container for storing Venn intersect results created by the `overLapper` function. The `setlist` slot stores the original label sets as `vectors` in a `list`; `intersectmatrix` organizes the label sets in a present-absent matrix; `complexitylevels` represents the number of comparisons considered for each comparison set as vector of integers; and `vennlist` contains the Venn intersect vectors.

### Objects from the Class

Objects can be created by calls of the form `new("VENNset", ...)`.

### Slots

`setlist`:

  Object of class `"list"`: `list` of `vectors`

`intersectmatrix`:

  Object of class `"matrix"`: binary `matrix`

`complexitylevels`:

  Object of class `"integer"`: `vector` of `integers`

`vennlist`:

  Object of class `"list"`: `list` of `vectors`

### Methods

as.list

  `signature(x = "VENNset")`: coerces `VENNset` to `list`

coerce

  `signature(from = "list", to = "VENNset")`: `as(list, "VENNset")`

complexitylevels

  `signature(x = "VENNset")`: extracts data from `complexitylevels` slot

intersectmatrix

  `signature(x = "VENNset")`: extracts data from `intersectmatrix` slot

length

  `signature(x = "VENNset")`: returns number of original label sets

names

  `signature(x = "VENNset")`: extracts slot names

setlist

  `signature(x = "VENNset")`: extracts data from `setlist` slot

show

  `signature(object = "VENNset")`: summary view of `VENNset` objects

vennlist

  `signature(x = "VENNset")`: extracts data from `vennset` slot

### Author(s)

Thomas Girke

### See Also

`overLapper`, `vennPlot`, `olBarplot`, `INTERSECTset-class`

### Examples

    showClass("VENNset")

    ## Sample data
    setlist <- list(A=sample(letters, 18), B=sample(letters, 16),
                    C=sample(letters, 20), D=sample(letters, 22),
                    E=sample(letters, 18), F=sample(letters, 22))

    ## Create VENNset
    vennset <- overLapper(setlist[1:5], type="vennsets")
    class(vennset)

    ## Accessor methods for VENNset/INTERSECTset objects
    names(vennset)
    setlist(vennset)
    intersectmatrix(vennset)
    complexitylevels(vennset)
    vennlist(vennset)

    ## Coerce VENNset/INTERSECTset object to list
    as.list(vennset)

[Package systemPipeR version 1.20.0 Index]