VENNset-class: Class '"VENNset"'

In systemPipeR: systemPipeR: NGS workflow and report generation environment

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)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.