 ## 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>,<ANY>,<ANY>,<ANY>)` ``[<-`(<TidySet>,<ANY>,<ANY>,<ANY>)` ``[[`(<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>)`
`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_elements()`
`add_relation()`
`add_relations()`
`add_sets()`
`adjacency(<TidySet>)` `adjacency_element()` `adjacency_set()` `adjacency(<TidySet>)`
`droplevels(<TidySet>)`
Drop unused elements and sets
`element_size()`
Calculates the size of the elements
`elements()` ``elements<-`()` `replace_elements()` `nElements(<TidySet>)`
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>,<characterORfactor>)`
Name elements
``name_sets<-`()`
Rename sets
`name_sets()` ``name_sets<-`(<TidySet>,<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>)`
Sets of the TidySet

Functions to read files in several formats

`getGAF()`
`getGMT()`
Import GMT (Gene Matrix Transposed) files
`getOBO()`

## dplyr functions

`arrange(<TidySet>)` `arrange_set()` `arrange_element()` `arrange_relation()`
Arrange the order of a TidySet
`filter(<TidySet>)` `filter_set()` `filter_element()` `filter_relation()`
Filter TidySet
`group_by(<TidySet>)`
group_by TidySet
`mutate(<TidySet>)` `mutate_set()` `mutate_element()` `mutate_relation()`
Mutate
`pull(<TidySet>)` `pull_set()` `pull_element()` `pull_relation()`
Pull from a TidySet
`select(<TidySet>)` `select_set()` `select_element()` `select_relation()`
select from a TidySet

## 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