Class "INTERSECTset"

Description

Container for storing standard 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 intersectlist contains the standard intersect vectors.

Objects from the Class

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

Slots

setlist:

Object of class "list": list of vectors

intersectmatrix:

Object of class "matrix": binary matrix

complexitylevels:

Object of class "integer": vector of integers

intersectlist:

Object of class "list": list of vectors

Methods

as.list

signature(x = "INTERSECTset"): coerces INTERSECTset to list

coerce

signature(from = "list", to = "INTERSECTset"): as(list, "INTERSECTset")

complexitylevels

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

intersectlist

signature(x = "INTERSECTset"): extracts data from intersectlist slot

intersectmatrix

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

length

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

names

signature(x = "INTERSECTset"): extracts slot names

setlist

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

show

signature(object = "INTERSECTset"): summary view of INTERSECTset objects

Author(s)

Thomas Girke

See Also

overLapper, vennPlot, olBarplot, VENNset-class

Examples

showClass("INTERSECTset")

## 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
interset <- overLapper(setlist[1:5], type="intersects")
class(interset)

## Accessor methods for VENNset/INTERSECTset objects
names(interset)
setlist(interset)
intersectmatrix(interset)
complexitylevels(interset)
intersectlist(interset)

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

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

Slots:
                                                                          
Name:           setlist  intersectmatrix complexitylevels    intersectlist
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
> interset <- overLapper(setlist[1:5], type="intersects")
> class(interset)
[1] "INTERSECTset"
attr(,"package")
[1] "systemPipeR"
> 
> ## Accessor methods for VENNset/INTERSECTset objects
> names(interset)
[1] "setlist"          "intersectmatrix"  "complexitylevels" "intersectlist"   
> setlist(interset)
$A
 [1] "a" "q" "k" "u" "f" "b" "e" "n" "p" "r" "z" "v" "c" "h" "s" "m" "x" "t"

$B
 [1] "w" "x" "t" "j" "l" "e" "z" "b" "f" "k" "m" "o" "a" "i" "u" "h"

$C
 [1] "x" "o" "l" "v" "z" "g" "y" "k" "a" "m" "c" "e" "n" "s" "d" "r" "u" "q" "j"
[20] "t"

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

$E
 [1] "b" "l" "s" "q" "c" "w" "z" "t" "x" "r" "d" "p" "g" "e" "f" "k" "i" "a"

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

$B
 [1] "a" "b" "e" "f" "h" "i" "j" "k" "l" "m" "o" "t" "u" "w" "x" "z"

$C
 [1] "a" "c" "d" "e" "g" "j" "k" "l" "m" "n" "o" "q" "r" "s" "t" "u" "v" "x" "y"
[20] "z"

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

$E
 [1] "a" "b" "c" "d" "e" "f" "g" "i" "k" "l" "p" "q" "r" "s" "t" "w" "x" "z"

$A_B
 [1] "a" "b" "e" "f" "h" "k" "m" "t" "u" "x" "z"

$A_C
 [1] "a" "c" "e" "k" "m" "n" "q" "r" "s" "t" "u" "v" "x" "z"

$A_D
 [1] "a" "b" "c" "e" "f" "k" "m" "n" "p" "q" "r" "t" "v" "x" "z"

$A_E
 [1] "a" "b" "c" "e" "f" "k" "p" "q" "r" "s" "t" "x" "z"

$B_C
 [1] "a" "e" "j" "k" "l" "m" "o" "t" "u" "x" "z"

$B_D
 [1] "a" "b" "e" "f" "i" "k" "l" "m" "o" "t" "w" "x" "z"

$B_E
 [1] "a" "b" "e" "f" "i" "k" "l" "t" "w" "x" "z"

$C_D
 [1] "a" "c" "d" "e" "g" "k" "l" "m" "n" "o" "q" "r" "t" "v" "x" "y" "z"

$C_E
 [1] "a" "c" "d" "e" "g" "k" "l" "q" "r" "s" "t" "x" "z"

$D_E
 [1] "a" "b" "c" "d" "e" "f" "g" "i" "k" "l" "p" "q" "r" "t" "w" "x" "z"

$A_B_C
[1] "a" "e" "k" "m" "t" "u" "x" "z"

$A_B_D
[1] "a" "b" "e" "f" "k" "m" "t" "x" "z"

$A_B_E
[1] "a" "b" "e" "f" "k" "t" "x" "z"

$A_C_D
 [1] "a" "c" "e" "k" "m" "n" "q" "r" "t" "v" "x" "z"

$A_C_E
 [1] "a" "c" "e" "k" "q" "r" "s" "t" "x" "z"

$A_D_E
 [1] "a" "b" "c" "e" "f" "k" "p" "q" "r" "t" "x" "z"

$B_C_D
[1] "a" "e" "k" "l" "m" "o" "t" "x" "z"

$B_C_E
[1] "a" "e" "k" "l" "t" "x" "z"

$B_D_E
 [1] "a" "b" "e" "f" "i" "k" "l" "t" "w" "x" "z"

$C_D_E
 [1] "a" "c" "d" "e" "g" "k" "l" "q" "r" "t" "x" "z"

$A_B_C_D
[1] "a" "e" "k" "m" "t" "x" "z"

$A_B_C_E
[1] "a" "e" "k" "t" "x" "z"

$A_B_D_E
[1] "a" "b" "e" "f" "k" "t" "x" "z"

$A_C_D_E
[1] "a" "c" "e" "k" "q" "r" "t" "x" "z"

$B_C_D_E
[1] "a" "e" "k" "l" "t" "x" "z"

$A_B_C_D_E
[1] "a" "e" "k" "t" "x" "z"

> 
> ## Coerce VENNset/INTERSECTset object to list
> as.list(interset)
$setlist
$setlist$A
 [1] "a" "q" "k" "u" "f" "b" "e" "n" "p" "r" "z" "v" "c" "h" "s" "m" "x" "t"

$setlist$B
 [1] "w" "x" "t" "j" "l" "e" "z" "b" "f" "k" "m" "o" "a" "i" "u" "h"

$setlist$C
 [1] "x" "o" "l" "v" "z" "g" "y" "k" "a" "m" "c" "e" "n" "s" "d" "r" "u" "q" "j"
[20] "t"

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

$setlist$E
 [1] "b" "l" "s" "q" "c" "w" "z" "t" "x" "r" "d" "p" "g" "e" "f" "k" "i" "a"


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

$intersectlist
$intersectlist$A
 [1] "a" "b" "c" "e" "f" "h" "k" "m" "n" "p" "q" "r" "s" "t" "u" "v" "x" "z"

$intersectlist$B
 [1] "a" "b" "e" "f" "h" "i" "j" "k" "l" "m" "o" "t" "u" "w" "x" "z"

$intersectlist$C
 [1] "a" "c" "d" "e" "g" "j" "k" "l" "m" "n" "o" "q" "r" "s" "t" "u" "v" "x" "y"
[20] "z"

$intersectlist$D
 [1] "a" "b" "c" "d" "e" "f" "g" "i" "k" "l" "m" "n" "o" "p" "q" "r" "t" "v" "w"
[20] "x" "y" "z"

$intersectlist$E
 [1] "a" "b" "c" "d" "e" "f" "g" "i" "k" "l" "p" "q" "r" "s" "t" "w" "x" "z"

$intersectlist$A_B
 [1] "a" "b" "e" "f" "h" "k" "m" "t" "u" "x" "z"

$intersectlist$A_C
 [1] "a" "c" "e" "k" "m" "n" "q" "r" "s" "t" "u" "v" "x" "z"

$intersectlist$A_D
 [1] "a" "b" "c" "e" "f" "k" "m" "n" "p" "q" "r" "t" "v" "x" "z"

$intersectlist$A_E
 [1] "a" "b" "c" "e" "f" "k" "p" "q" "r" "s" "t" "x" "z"

$intersectlist$B_C
 [1] "a" "e" "j" "k" "l" "m" "o" "t" "u" "x" "z"

$intersectlist$B_D
 [1] "a" "b" "e" "f" "i" "k" "l" "m" "o" "t" "w" "x" "z"

$intersectlist$B_E
 [1] "a" "b" "e" "f" "i" "k" "l" "t" "w" "x" "z"

$intersectlist$C_D
 [1] "a" "c" "d" "e" "g" "k" "l" "m" "n" "o" "q" "r" "t" "v" "x" "y" "z"

$intersectlist$C_E
 [1] "a" "c" "d" "e" "g" "k" "l" "q" "r" "s" "t" "x" "z"

$intersectlist$D_E
 [1] "a" "b" "c" "d" "e" "f" "g" "i" "k" "l" "p" "q" "r" "t" "w" "x" "z"

$intersectlist$A_B_C
[1] "a" "e" "k" "m" "t" "u" "x" "z"

$intersectlist$A_B_D
[1] "a" "b" "e" "f" "k" "m" "t" "x" "z"

$intersectlist$A_B_E
[1] "a" "b" "e" "f" "k" "t" "x" "z"

$intersectlist$A_C_D
 [1] "a" "c" "e" "k" "m" "n" "q" "r" "t" "v" "x" "z"

$intersectlist$A_C_E
 [1] "a" "c" "e" "k" "q" "r" "s" "t" "x" "z"

$intersectlist$A_D_E
 [1] "a" "b" "c" "e" "f" "k" "p" "q" "r" "t" "x" "z"

$intersectlist$B_C_D
[1] "a" "e" "k" "l" "m" "o" "t" "x" "z"

$intersectlist$B_C_E
[1] "a" "e" "k" "l" "t" "x" "z"

$intersectlist$B_D_E
 [1] "a" "b" "e" "f" "i" "k" "l" "t" "w" "x" "z"

$intersectlist$C_D_E
 [1] "a" "c" "d" "e" "g" "k" "l" "q" "r" "t" "x" "z"

$intersectlist$A_B_C_D
[1] "a" "e" "k" "m" "t" "x" "z"

$intersectlist$A_B_C_E
[1] "a" "e" "k" "t" "x" "z"

$intersectlist$A_B_D_E
[1] "a" "b" "e" "f" "k" "t" "x" "z"

$intersectlist$A_C_D_E
[1] "a" "c" "e" "k" "q" "r" "t" "x" "z"

$intersectlist$B_C_D_E
[1] "a" "e" "k" "l" "t" "x" "z"

$intersectlist$A_B_C_D_E
[1] "a" "e" "k" "t" "x" "z"


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