Working with Sets the Tidy Way

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Documentation for package ‘BaseSet’ version 0.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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A C D E F G I L M N P R S T U misc

-- A --

activate	Determine the context of subsequent manipulations.
active	Determine the context of subsequent manipulations.
add_column	Add column
add_column-method	Add column
add_elements	Add elements to a TidySet
add_relation	Add relations
add_relation-method	Add relations
add_relations	Add relations to a TidySet
add_sets	Add sets to a TidySet
adjacency	Adjacency
adjacency.TidySet	Adjacency
adjacency_element	Adjacency
adjacency_set	Adjacency
arrange.TidySet	Arrange the order of a TidySet
arrange_element	Arrange the order of a TidySet
arrange_relation	Arrange the order of a TidySet
arrange_set	Arrange the order of a TidySet
as.data.frame.TidySet	Transforms a TidySet to a data.frame
as.list.TidySet	Convert to list

-- C --

c-method	Combine Values into a Vector or List
cardinality	Cardinality or membership of sets
cardinality-method	Cardinality or membership of sets
cartesian	Create the cartesian product of two sets
cartesian.TidySet	Create the cartesian product of two sets
complement	Complement TidySet
complement_element	Complement of elements
complement_element-method	Complement of elements
complement_set	Complement of a set
complement_set-method	Complement of a set

-- D --

deactivate	Determine the context of subsequent manipulations.
droplevels.TidySet	Drop unused elements and sets

-- E --

elements	Elements of the TidySet
elements-method	Elements of the TidySet
elements<-	Elements of the TidySet
elements<--method	Elements of the TidySet
element_size	Calculates the size of the elements
element_size-method	Calculates the size of the elements
extract-TidySet	Extract

-- F --

filter.TidySet	Filter TidySet
filter_element	Filter TidySet
filter_relation	Filter TidySet
filter_set	Filter TidySet

-- G --

getGAF	Read a GAF file
getGMT	Import GMT (Gene Matrix Transposed) files
getOBO	Read an OBO file
group	Create a new set from existing elements
group.TidySet	Create a new set from existing elements
group_by.TidySet	group_by TidySet

-- I --

incidence	Incidence
incidence-method	Incidence
independent	Independence of the sets
independent_probabilities	Probability of a vector of probabilities
intersect	Intersection of two or more sets
intersection	Intersection of two or more sets
intersection-method	Intersection of two or more sets
is.fuzzy	Check if a TidySet is fuzzy.
is.fuzzy-method	Check if a TidySet is fuzzy.
is_nested	Are some sets as elements of other sets?
is_nested.TidySet	Are some sets as elements of other sets?

-- L --

length.TidySet	Length of the TidySet
lengths-method	Lengths of the TidySet
length_probability	Calculates the probability of a single length
length_set	Calculates the probability

-- M --

move_to	Move columns between slots
move_to-method	Move columns between slots
multiply_probabilities	Probability of a vector of probabilities
mutate.TidySet	Mutate
mutate_element	Mutate
mutate_relation	Mutate
mutate_set	Mutate

-- N --

name_elements	Name elements
name_elements-method	Name elements
name_elements<-	Rename elements
name_elements<--method	Name elements
name_sets	Name sets
name_sets-method	Name sets
name_sets<-	Rename sets
name_sets<--method	Name sets
naming	Name an operation
nElements	Number of elements
nElements-method	Elements of the TidySet
nRelations	Number of relations
nRelations-method	Relations of the TidySet
nSets	Number of sets
nSets-method	Sets of the TidySet

-- P --

power_set	Create the power set
pull.TidySet	Pull from a TidySet
pull_element	Pull from a TidySet
pull_relation	Pull from a TidySet
pull_set	Pull from a TidySet

-- R --

relations	Relations of the TidySet
relations-method	Relations of the TidySet
relations<-	Relations of the TidySet
relations<--method	Relations of the TidySet
remove_column	Remove column
remove_column-method	Remove column
remove_element	Remove elements
remove_element-method	Remove elements
remove_relation	Remove a relation
remove_relation-method	Remove a relation
remove_set	Remove sets
remove_set-method	Remove sets
rename_elements	Rename elements
rename_elements-method	Rename elements
rename_set	Rename sets
rename_set-method	Rename sets
replace_elements	Elements of the TidySet
replace_relations	Relations of the TidySet
replace_sets	Sets of the TidySet

-- S --

select.TidySet	select from a TidySet
select_element	select from a TidySet
select_relation	select from a TidySet
select_set	select from a TidySet
sets	Sets of the TidySet
sets-method	Sets of the TidySet
sets<-	Sets of the TidySet
sets<--method	Sets of the TidySet
set_size	Calculates the size of a set
set_size-method	Calculates the size of a set
set_symbols	A subset of symbols related to sets
show-method	Method to show the TidySet object
size	Size
subtract	Subtract
subtract-method	Subtract

-- T --

tidy	Convert GSEABase classes to a TidySet
tidy.GeneSet	Convert GSEABase classes to a TidySet
tidy.GeneSetCollection	Convert GSEABase classes to a TidySet
TidySet	A tidy class to represent a set
tidySet	Create a TidySet object
TidySet-class	A tidy class to represent a set
tidySet.data.frame	Create a TidySet object
tidySet.Go3AnnDbBimap	Create a TidySet object
tidySet.list	Create a TidySet object
tidySet.matrix	Create a TidySet object
tidySet.TidySet	Create a TidySet object

-- U --

union	Join sets
union.TidySet	Join sets
union_closed	Union closed sets
union_closed.TidySet	Union closed sets
union_probability	Calculates the probability of a single length

-- misc --

$-method	Extract
$<--method	Extract
[-method	Extract
[<--method	Extract
[[-method	Extract
[[<--method	Extract