Class "INTERSECTset"

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

Thomas Girke

See also

overLapper, vennPlot, olBarplot, VENNset-class

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] "z" "l" "v" "k" "a" "r" "p" "m" "i" "t" "h" "j" "u" "f" "x" "e" "n" "c"
#> 
#> $B
#>  [1] "q" "x" "o" "i" "b" "g" "s" "h" "e" "l" "f" "j" "k" "v" "z" "c"
#> 
#> $C
#>  [1] "g" "h" "b" "q" "r" "z" "c" "s" "y" "d" "j" "x" "o" "n" "e" "f" "k" "w" "a"
#> [20] "v"
#> 
#> $D
#>  [1] "x" "p" "j" "w" "v" "n" "y" "u" "t" "g" "k" "c" "a" "q" "o" "i" "e" "s" "l"
#> [20] "h" "z" "m"
#> 
#> $E
#>  [1] "t" "e" "v" "y" "o" "z" "p" "g" "n" "i" "w" "a" "u" "x" "j" "h" "r" "m"
#> 
intersectmatrix(interset)
#>   A B C D E
#> a 1 0 1 1 1
#> b 0 1 1 0 0
#> c 1 1 1 1 0
#> d 0 0 1 0 0
#> e 1 1 1 1 1
#> f 1 1 1 0 0
#> g 0 1 1 1 1
#> h 1 1 1 1 1
#> i 1 1 0 1 1
#> j 1 1 1 1 1
#> k 1 1 1 1 0
#> l 1 1 0 1 0
#> m 1 0 0 1 1
#> n 1 0 1 1 1
#> o 0 1 1 1 1
#> p 1 0 0 1 1
#> q 0 1 1 1 0
#> r 1 0 1 0 1
#> s 0 1 1 1 0
#> t 1 0 0 1 1
#> u 1 0 0 1 1
#> v 1 1 1 1 1
#> w 0 0 1 1 1
#> x 1 1 1 1 1
#> y 0 0 1 1 1
#> 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" "c" "e" "f" "h" "i" "j" "k" "l" "m" "n" "p" "r" "t" "u" "v" "x" "z"
#> 
#> $B
#>  [1] "b" "c" "e" "f" "g" "h" "i" "j" "k" "l" "o" "q" "s" "v" "x" "z"
#> 
#> $C
#>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "j" "k" "n" "o" "q" "r" "s" "v" "w" "x" "y"
#> [20] "z"
#> 
#> $D
#>  [1] "a" "c" "e" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "s" "t" "u" "v" "w"
#> [20] "x" "y" "z"
#> 
#> $E
#>  [1] "a" "e" "g" "h" "i" "j" "m" "n" "o" "p" "r" "t" "u" "v" "w" "x" "y" "z"
#> 
#> $A_B
#>  [1] "c" "e" "f" "h" "i" "j" "k" "l" "v" "x" "z"
#> 
#> $A_C
#>  [1] "a" "c" "e" "f" "h" "j" "k" "n" "r" "v" "x" "z"
#> 
#> $A_D
#>  [1] "a" "c" "e" "h" "i" "j" "k" "l" "m" "n" "p" "t" "u" "v" "x" "z"
#> 
#> $A_E
#>  [1] "a" "e" "h" "i" "j" "m" "n" "p" "r" "t" "u" "v" "x" "z"
#> 
#> $B_C
#>  [1] "b" "c" "e" "f" "g" "h" "j" "k" "o" "q" "s" "v" "x" "z"
#> 
#> $B_D
#>  [1] "c" "e" "g" "h" "i" "j" "k" "l" "o" "q" "s" "v" "x" "z"
#> 
#> $B_E
#> [1] "e" "g" "h" "i" "j" "o" "v" "x" "z"
#> 
#> $C_D
#>  [1] "a" "c" "e" "g" "h" "j" "k" "n" "o" "q" "s" "v" "w" "x" "y" "z"
#> 
#> $C_E
#>  [1] "a" "e" "g" "h" "j" "n" "o" "r" "v" "w" "x" "y" "z"
#> 
#> $D_E
#>  [1] "a" "e" "g" "h" "i" "j" "m" "n" "o" "p" "t" "u" "v" "w" "x" "y" "z"
#> 
#> $A_B_C
#> [1] "c" "e" "f" "h" "j" "k" "v" "x" "z"
#> 
#> $A_B_D
#>  [1] "c" "e" "h" "i" "j" "k" "l" "v" "x" "z"
#> 
#> $A_B_E
#> [1] "e" "h" "i" "j" "v" "x" "z"
#> 
#> $A_C_D
#>  [1] "a" "c" "e" "h" "j" "k" "n" "v" "x" "z"
#> 
#> $A_C_E
#> [1] "a" "e" "h" "j" "n" "r" "v" "x" "z"
#> 
#> $A_D_E
#>  [1] "a" "e" "h" "i" "j" "m" "n" "p" "t" "u" "v" "x" "z"
#> 
#> $B_C_D
#>  [1] "c" "e" "g" "h" "j" "k" "o" "q" "s" "v" "x" "z"
#> 
#> $B_C_E
#> [1] "e" "g" "h" "j" "o" "v" "x" "z"
#> 
#> $B_D_E
#> [1] "e" "g" "h" "i" "j" "o" "v" "x" "z"
#> 
#> $C_D_E
#>  [1] "a" "e" "g" "h" "j" "n" "o" "v" "w" "x" "y" "z"
#> 
#> $A_B_C_D
#> [1] "c" "e" "h" "j" "k" "v" "x" "z"
#> 
#> $A_B_C_E
#> [1] "e" "h" "j" "v" "x" "z"
#> 
#> $A_B_D_E
#> [1] "e" "h" "i" "j" "v" "x" "z"
#> 
#> $A_C_D_E
#> [1] "a" "e" "h" "j" "n" "v" "x" "z"
#> 
#> $B_C_D_E
#> [1] "e" "g" "h" "j" "o" "v" "x" "z"
#> 
#> $A_B_C_D_E
#> [1] "e" "h" "j" "v" "x" "z"
#> 

## Coerce VENNset/INTERSECTset object to list
as.list(interset)
#> $setlist
#> $setlist$A
#>  [1] "z" "l" "v" "k" "a" "r" "p" "m" "i" "t" "h" "j" "u" "f" "x" "e" "n" "c"
#> 
#> $setlist$B
#>  [1] "q" "x" "o" "i" "b" "g" "s" "h" "e" "l" "f" "j" "k" "v" "z" "c"
#> 
#> $setlist$C
#>  [1] "g" "h" "b" "q" "r" "z" "c" "s" "y" "d" "j" "x" "o" "n" "e" "f" "k" "w" "a"
#> [20] "v"
#> 
#> $setlist$D
#>  [1] "x" "p" "j" "w" "v" "n" "y" "u" "t" "g" "k" "c" "a" "q" "o" "i" "e" "s" "l"
#> [20] "h" "z" "m"
#> 
#> $setlist$E
#>  [1] "t" "e" "v" "y" "o" "z" "p" "g" "n" "i" "w" "a" "u" "x" "j" "h" "r" "m"
#> 
#> 
#> $intersectmatrix
#>   A B C D E
#> a 1 0 1 1 1
#> b 0 1 1 0 0
#> c 1 1 1 1 0
#> d 0 0 1 0 0
#> e 1 1 1 1 1
#> f 1 1 1 0 0
#> g 0 1 1 1 1
#> h 1 1 1 1 1
#> i 1 1 0 1 1
#> j 1 1 1 1 1
#> k 1 1 1 1 0
#> l 1 1 0 1 0
#> m 1 0 0 1 1
#> n 1 0 1 1 1
#> o 0 1 1 1 1
#> p 1 0 0 1 1
#> q 0 1 1 1 0
#> r 1 0 1 0 1
#> s 0 1 1 1 0
#> t 1 0 0 1 1
#> u 1 0 0 1 1
#> v 1 1 1 1 1
#> w 0 0 1 1 1
#> x 1 1 1 1 1
#> y 0 0 1 1 1
#> 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" "c" "e" "f" "h" "i" "j" "k" "l" "m" "n" "p" "r" "t" "u" "v" "x" "z"
#> 
#> $intersectlist$B
#>  [1] "b" "c" "e" "f" "g" "h" "i" "j" "k" "l" "o" "q" "s" "v" "x" "z"
#> 
#> $intersectlist$C
#>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "j" "k" "n" "o" "q" "r" "s" "v" "w" "x" "y"
#> [20] "z"
#> 
#> $intersectlist$D
#>  [1] "a" "c" "e" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "s" "t" "u" "v" "w"
#> [20] "x" "y" "z"
#> 
#> $intersectlist$E
#>  [1] "a" "e" "g" "h" "i" "j" "m" "n" "o" "p" "r" "t" "u" "v" "w" "x" "y" "z"
#> 
#> $intersectlist$A_B
#>  [1] "c" "e" "f" "h" "i" "j" "k" "l" "v" "x" "z"
#> 
#> $intersectlist$A_C
#>  [1] "a" "c" "e" "f" "h" "j" "k" "n" "r" "v" "x" "z"
#> 
#> $intersectlist$A_D
#>  [1] "a" "c" "e" "h" "i" "j" "k" "l" "m" "n" "p" "t" "u" "v" "x" "z"
#> 
#> $intersectlist$A_E
#>  [1] "a" "e" "h" "i" "j" "m" "n" "p" "r" "t" "u" "v" "x" "z"
#> 
#> $intersectlist$B_C
#>  [1] "b" "c" "e" "f" "g" "h" "j" "k" "o" "q" "s" "v" "x" "z"
#> 
#> $intersectlist$B_D
#>  [1] "c" "e" "g" "h" "i" "j" "k" "l" "o" "q" "s" "v" "x" "z"
#> 
#> $intersectlist$B_E
#> [1] "e" "g" "h" "i" "j" "o" "v" "x" "z"
#> 
#> $intersectlist$C_D
#>  [1] "a" "c" "e" "g" "h" "j" "k" "n" "o" "q" "s" "v" "w" "x" "y" "z"
#> 
#> $intersectlist$C_E
#>  [1] "a" "e" "g" "h" "j" "n" "o" "r" "v" "w" "x" "y" "z"
#> 
#> $intersectlist$D_E
#>  [1] "a" "e" "g" "h" "i" "j" "m" "n" "o" "p" "t" "u" "v" "w" "x" "y" "z"
#> 
#> $intersectlist$A_B_C
#> [1] "c" "e" "f" "h" "j" "k" "v" "x" "z"
#> 
#> $intersectlist$A_B_D
#>  [1] "c" "e" "h" "i" "j" "k" "l" "v" "x" "z"
#> 
#> $intersectlist$A_B_E
#> [1] "e" "h" "i" "j" "v" "x" "z"
#> 
#> $intersectlist$A_C_D
#>  [1] "a" "c" "e" "h" "j" "k" "n" "v" "x" "z"
#> 
#> $intersectlist$A_C_E
#> [1] "a" "e" "h" "j" "n" "r" "v" "x" "z"
#> 
#> $intersectlist$A_D_E
#>  [1] "a" "e" "h" "i" "j" "m" "n" "p" "t" "u" "v" "x" "z"
#> 
#> $intersectlist$B_C_D
#>  [1] "c" "e" "g" "h" "j" "k" "o" "q" "s" "v" "x" "z"
#> 
#> $intersectlist$B_C_E
#> [1] "e" "g" "h" "j" "o" "v" "x" "z"
#> 
#> $intersectlist$B_D_E
#> [1] "e" "g" "h" "i" "j" "o" "v" "x" "z"
#> 
#> $intersectlist$C_D_E
#>  [1] "a" "e" "g" "h" "j" "n" "o" "v" "w" "x" "y" "z"
#> 
#> $intersectlist$A_B_C_D
#> [1] "c" "e" "h" "j" "k" "v" "x" "z"
#> 
#> $intersectlist$A_B_C_E
#> [1] "e" "h" "j" "v" "x" "z"
#> 
#> $intersectlist$A_B_D_E
#> [1] "e" "h" "i" "j" "v" "x" "z"
#> 
#> $intersectlist$A_C_D_E
#> [1] "a" "e" "h" "j" "n" "v" "x" "z"
#> 
#> $intersectlist$B_C_D_E
#> [1] "e" "g" "h" "j" "o" "v" "x" "z"
#> 
#> $intersectlist$A_B_C_D_E
#> [1] "e" "h" "j" "v" "x" "z"
#> 
#>