listOverlapCoefficient: Pairwise overlap coefficient of lists

In ribiosUtils: Utilities from and Interface to the Bioinfo-C (BIOS) Library

Description

Pairwise overlap coefficient of lists

Usage

listOverlapCoefficient(x, y = NULL, checkUniqueNonNA = TRUE)

Arguments

x	A list of vectors that are interpreted as sets of elements
y	A list of vectors that are interpreted as sets of elements. In case of NULL, pairwise overlap coefficient of lists in x is returned.
checkUniqueNonNA	Logical, should vectors in the list be first cleaned up so that NA values are removed and the elements are made unique? Default is set as TRUE; if the user is confident that the vectors are indeed valid sets, this option can be set as FALSE to speed up the code

Value

A matrix of column-wise pairwise overlap coefficients.

Examples

set.seed(1887)
testSets1 <- sapply(rbinom(10, size=26, prob=0.3), 
  function(x) sample(LETTERS, x, replace=FALSE))
names(testSets1) <- sprintf("List%d", seq(along=testSets1))
testSets1Poe <- listOverlapCoefficient(testSets1)
testSets1PoeNoCheck <- listOverlapCoefficient(testSets1, checkUniqueNonNA=FALSE)
stopifnot(identical(testSets1Poe, testSets1PoeNoCheck))

testSets2 <- sapply(rbinom(15, size=26, prob=0.3),
  function(x) sample(LETTERS, x, replace=FALSE))
names(testSets2) <- sprintf("AnotherList%d", seq(along=testSets2))
testSets12Poe <- listOverlapCoefficient(testSets1, testSets2)

ribiosUtils documentation built on March 13, 2020, 2:54 a.m.