# Working with Sets the Tidy Way

## Documentation for package ‘BaseSet’ version 0.9.0

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

## Help Pages

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