VENNset-class: Class '"VENNset"'

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

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)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.