Sets-class: Sets Class
In kevinrue/unisets: Collection of Classes to Store Gene Sets

Description Usage Arguments Value Slots Author(s) See Also Examples

The Sets class implements a container to describe distinct objects that make up sets, along with element metadata and set metadata.

1 2	Sets(relations = DataFrame(element = character(0), set = character(0)), elementInfo, setInfo)

`relations`	`DataFrame`. At least two columns that provide mapping relationships between `"element"` and `"set"` identifiers. Additional columns are taken as relation metadata.
`elementInfo`	`IdVector`. Metadata for each unique identifier in `relations$element` is provided as `mcols(elementInfo)`.
`setInfo`	`IdVector`. Metadata for each unique identifier in `relations$set` is provided as `mcols(setInfo)`.

A Sets object.

relations: Hits The left node and right node of each hit stores the index of the element and set in elementInfo and setInfo, respectively. Metadata for each relation is stored as mcols(relations(object)).
elementInfo: IdVector. Metadata for each unique element in relations$element is stored as mcols(elementInfo).
setInfo: IdVector. Metadata for each unique set in relations$set is stored as mcols(setInfo).

Kevin Rue-Albrecht

Sets-methods.

# Constructor ----

# Visually intuitive definition of sets
sets <- list(
  set1=c("A", "B"),
  set2=c("B", "C", "D"),
  set3=c("E"))

bs <- as(sets, "Sets")
bs

# Coercing ----

# to list (gene sets)
ls1 <- as(bs, "list")
ls1
# to matrix (logical membership)
m1 <- as(bs, "matrix")
m1

# Accessors ----

relations(bs)
elementInfo(bs)
setInfo(bs)

# Dimensions ----

length(bs)
nElements(bs)
nSets(bs)

setLengths(bs)
elementLengths(bs)