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

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

The FuzzySets class extends the Sets class to implement a container that also describe different grades of membership in the interval [0,1].

1 2	FuzzySets(relations = DataFrame(element = character(0), set = character(0), membership = numeric(0)), ...)

`relations`	`DataFrame`. At least 3 columns that provide mapping relationships between `"element"` and `"set"` identifiers, with `"membership"` function in the range `[0,1]`. Additional columns are taken as relation metadata.
`...`	Arguments passed to the `Sets()` constructor and other functions.

This class does not define any additional slot to the Sets class. However, this class defines additional validity checks to ensure that every relation stored in a FuzzySets are associated with a numeric membership funtion in the interval [0,1].

A FuzzySets object.

Kevin Rue-Albrecht

Sets, FuzzyHits, FuzzySets-methods.

# Constructor ----

# Visually intuitive definition of sets, elements, and membership
sets <- list(
  set1=c("A"=0.1, "B"=0.2),
  set2=c("B"=0.3, "C"=0.4, "D"=0.5),
  set3=c("E"=0.8))

# unlist the set names
unlistSets <- rep(names(sets), lengths(sets))
# unlist the element names
unlistElements <- unlist(sapply(sets, names))
# unlist the membership values
unlistMembership <- unlist(sets)

# Reformat as a table
relations <- DataFrame(
  element=unlistElements,
  set=unlistSets,
  membership=unlistMembership
)

fs <- FuzzySets(relations=relations)

# Subsetting ----

fs1 <- subset(fs, set == "set1" | membership > 0.5)

# Coercing ----

# to list (gene sets)
ls1 <- as(fs, "list")
# to matrix (continuous membership)
m1 <- as(fs, "matrix")
# to matrix (multiple observations)
mm1 <- as.matrix(fs, fun.aggregate=min)

# Getters/Setters ----

membership(fs)

fs1 <- fs
membership(fs1) <- runif(length(fs1))