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General

Functions to create a TidySet from other formats

BaseSet BaseSet-package
BaseSet: Working with Sets the Tidy Way
tidySet()
Create a TidySet object
tidy()
Convert GSEABase classes to a TidySet
as.data.frame(<TidySet>)
Transforms a TidySet to a data.frame
as.list(<TidySet>)
Convert to list
incidence()
Incidence

R operations

Functions to use TidySets

c(<TidySet>)
Combine Values into a Vector or List
`$`(<TidySet>) `$<-`(<TidySet>) `[`(<TidySet>) `[<-`(<TidySet>) `[[`(<TidySet>) `[[<-`(<TidySet>)
Extract
length(<TidySet>)
Length of the TidySet
lengths(<TidySet>)
Lengths of the TidySet
dimnames(<TidySet>)
Dimnames of a TidySet
names(<TidySet>)
Names of a TidySet
show(<TidySet>)
Method to show the TidySet object

Set operations

Functions to perform set operations

adjacency(<TidySet>) adjacency_element() adjacency_set() adjacency(<TidySet>)
Adjacency
cartesian()
Create the cartesian product of two sets
cardinality()
Cardinality or membership of sets
complement()
Complement TidySet
complement_element()
Complement of elements
complement_set()
Complement of a set
incidence()
Incidence
independent()
Independence of the sets
intersection()
Intersection of two or more sets
is.fuzzy()
Check if a TidySet is fuzzy.
power_set()
Create the power set
size()
Size
subtract()
Subtract
union()
Join sets

Working with TidySet

TidySet-class TidySet
A tidy class to represent a set
activate() active() deactivate()
Determine the context of subsequent manipulations.
add_column()
Add column
add_elements()
Add elements to a TidySet
add_relation()
Add relations
add_relations()
Add relations to a TidySet
add_sets()
Add sets to a TidySet
adjacency(<TidySet>) adjacency_element() adjacency_set() adjacency(<TidySet>)
Adjacency
droplevels(<TidySet>)
Drop unused elements and sets
element_size()
Calculates the size of the elements
elements() `elements<-`() replace_elements() nElements(<TidySet>,<missing>) nElements(<TidySet>,<logical>)
Elements of the TidySet
group()
Create a new set from existing elements
is_nested()
Are some sets as elements of other sets?
nElements()
Number of elements
nRelations()
Number of relations
nSets()
Number of sets
move_to()
Move columns between slots
`name_elements<-`()
Rename elements
name_elements() `name_elements<-`(<TidySet>,<logical>,<characterORfactor>) `name_elements<-`(<TidySet>,<missing>,<characterORfactor>)
Name elements
`name_sets<-`()
Rename sets
name_sets() `name_sets<-`(<TidySet>,<logical>,<characterORfactor>) `name_sets<-`(<TidySet>,<missing>,<characterORfactor>)
Name sets
remove_column()
Remove column
remove_element()
Remove elements
remove_relation()
Remove a relation
remove_set()
Remove sets
rename_elements()
Rename elements
rename_set()
Rename sets
relations() `relations<-`() replace_relations() nRelations(<TidySet>)
Relations of the TidySet
set_size()
Calculates the size of a set
sets() `sets<-`() replace_sets() nSets(<TidySet>,<missing>) nSets(<TidySet>,<logical>)
Sets of the TidySet

Reading files

Functions to read files in several formats

getGAF()
Read a GAF file
getGMT()
Import GMT (Gene Matrix Transposed) files
getOBO()
Read an OBO file

dplyr functions

Utiles

Functions or data to help or show how to work with sets

naming()
Name an operation
set_symbols
A subset of symbols related to sets
length_set()
Calculates the probability
union_probability() length_probability()
Calculates the probability of a single length
union_closed()
Union closed sets
multiply_probabilities() independent_probabilities()
Probability of a vector of probabilities