General

Functions to create a TidySet from other formats

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

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

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>)

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

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

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

show(<TidySet>)

Method to show the TidySet object

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

multiply_probabilities() independent_probabilities()

Probability of a vector of probabilities