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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/systemPipeR/VENNset-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: VENNset-class
> ### Title: Class '"VENNset"'
> ### Aliases: VENNset-class as.list,VENNset-method
> ###   coerce,list,VENNset-method complexitylevels,VENNset-method
> ###   intersectmatrix,VENNset-method length,VENNset-method
> ###   names,VENNset-method setlist,VENNset-method show,VENNset-method
> ###   vennlist,VENNset-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("VENNset")
Class "VENNset" [package "systemPipeR"]

Slots:
                                                                          
Name:           setlist  intersectmatrix complexitylevels         vennlist
Class:             list           matrix          integer             list
> 
> ## 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)
[1] "VENNset"
attr(,"package")
[1] "systemPipeR"
> 
> ## Accessor methods for VENNset/INTERSECTset objects
> names(vennset)
[1] "setlist"          "intersectmatrix"  "complexitylevels" "vennlist"        
> setlist(vennset)
$A
 [1] "c" "e" "m" "u" "y" "h" "d" "r" "a" "q" "b" "o" "n" "t" "l" "s" "j" "g"

$B
 [1] "u" "v" "p" "b" "z" "x" "s" "l" "j" "y" "c" "h" "d" "m" "i" "g"

$C
 [1] "g" "d" "e" "x" "w" "s" "k" "a" "i" "b" "c" "m" "f" "q" "j" "r" "o" "l" "t"
[20] "z"

$D
 [1] "a" "z" "f" "i" "j" "b" "g" "v" "q" "n" "e" "p" "k" "c" "w" "o" "h" "y" "r"
[20] "s" "m" "l"

$E
 [1] "v" "j" "s" "c" "d" "b" "f" "z" "h" "m" "l" "k" "o" "q" "i" "r" "w" "g"

> intersectmatrix(vennset)
  A B C D E
a 1 0 1 1 0
b 1 1 1 1 1
c 1 1 1 1 1
d 1 1 1 0 1
e 1 0 1 1 0
f 0 0 1 1 1
g 1 1 1 1 1
h 1 1 0 1 1
i 0 1 1 1 1
j 1 1 1 1 1
k 0 0 1 1 1
l 1 1 1 1 1
m 1 1 1 1 1
n 1 0 0 1 0
o 1 0 1 1 1
p 0 1 0 1 0
q 1 0 1 1 1
r 1 0 1 1 1
s 1 1 1 1 1
t 1 0 1 0 0
u 1 1 0 0 0
v 0 1 0 1 1
w 0 0 1 1 1
x 0 1 1 0 0
y 1 1 0 1 0
z 0 1 1 1 1
> complexitylevels(vennset)
 [1] 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 5
> vennlist(vennset)
$A
character(0)

$B
character(0)

$C
character(0)

$D
character(0)

$E
character(0)

$A_B
[1] "u"

$A_C
[1] "t"

$A_D
[1] "n"

$A_E
character(0)

$B_C
[1] "x"

$B_D
[1] "p"

$B_E
character(0)

$C_D
character(0)

$C_E
character(0)

$D_E
character(0)

$A_B_C
character(0)

$A_B_D
[1] "y"

$A_B_E
character(0)

$A_C_D
[1] "a" "e"

$A_C_E
character(0)

$A_D_E
character(0)

$B_C_D
character(0)

$B_C_E
character(0)

$B_D_E
[1] "v"

$C_D_E
[1] "f" "k" "w"

$A_B_C_D
character(0)

$A_B_C_E
[1] "d"

$A_B_D_E
[1] "h"

$A_C_D_E
[1] "o" "q" "r"

$B_C_D_E
[1] "i" "z"

$A_B_C_D_E
[1] "b" "c" "g" "j" "l" "m" "s"

> 
> ## Coerce VENNset/INTERSECTset object to list
> as.list(vennset)
$setlist
$setlist$A
 [1] "c" "e" "m" "u" "y" "h" "d" "r" "a" "q" "b" "o" "n" "t" "l" "s" "j" "g"

$setlist$B
 [1] "u" "v" "p" "b" "z" "x" "s" "l" "j" "y" "c" "h" "d" "m" "i" "g"

$setlist$C
 [1] "g" "d" "e" "x" "w" "s" "k" "a" "i" "b" "c" "m" "f" "q" "j" "r" "o" "l" "t"
[20] "z"

$setlist$D
 [1] "a" "z" "f" "i" "j" "b" "g" "v" "q" "n" "e" "p" "k" "c" "w" "o" "h" "y" "r"
[20] "s" "m" "l"

$setlist$E
 [1] "v" "j" "s" "c" "d" "b" "f" "z" "h" "m" "l" "k" "o" "q" "i" "r" "w" "g"


$intersectmatrix
  A B C D E
a 1 0 1 1 0
b 1 1 1 1 1
c 1 1 1 1 1
d 1 1 1 0 1
e 1 0 1 1 0
f 0 0 1 1 1
g 1 1 1 1 1
h 1 1 0 1 1
i 0 1 1 1 1
j 1 1 1 1 1
k 0 0 1 1 1
l 1 1 1 1 1
m 1 1 1 1 1
n 1 0 0 1 0
o 1 0 1 1 1
p 0 1 0 1 0
q 1 0 1 1 1
r 1 0 1 1 1
s 1 1 1 1 1
t 1 0 1 0 0
u 1 1 0 0 0
v 0 1 0 1 1
w 0 0 1 1 1
x 0 1 1 0 0
y 1 1 0 1 0
z 0 1 1 1 1

$complexitylevels
 [1] 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 5

$vennlist
$vennlist$A
character(0)

$vennlist$B
character(0)

$vennlist$C
character(0)

$vennlist$D
character(0)

$vennlist$E
character(0)

$vennlist$A_B
[1] "u"

$vennlist$A_C
[1] "t"

$vennlist$A_D
[1] "n"

$vennlist$A_E
character(0)

$vennlist$B_C
[1] "x"

$vennlist$B_D
[1] "p"

$vennlist$B_E
character(0)

$vennlist$C_D
character(0)

$vennlist$C_E
character(0)

$vennlist$D_E
character(0)

$vennlist$A_B_C
character(0)

$vennlist$A_B_D
[1] "y"

$vennlist$A_B_E
character(0)

$vennlist$A_C_D
[1] "a" "e"

$vennlist$A_C_E
character(0)

$vennlist$A_D_E
character(0)

$vennlist$B_C_D
character(0)

$vennlist$B_C_E
character(0)

$vennlist$B_D_E
[1] "v"

$vennlist$C_D_E
[1] "f" "k" "w"

$vennlist$A_B_C_D
character(0)

$vennlist$A_B_C_E
[1] "d"

$vennlist$A_B_D_E
[1] "h"

$vennlist$A_C_D_E
[1] "o" "q" "r"

$vennlist$B_C_D_E
[1] "i" "z"

$vennlist$A_B_C_D_E
[1] "b" "c" "g" "j" "l" "m" "s"


> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>