Package index • BaseSet

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

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

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

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