jaccard: Calculate the Jaccard index between all columns in a matrix

In skinnider/dismay: dismay: distance metrics for matrices

Description

Calculate the Jaccard index between all pairs of columns in a matrix. The Jaccard index (also known as the Tanimoto coefficient) is defined as the size of the intersection of two bitsets divided by the size of the union. Here, to convert a list of continuous expression values into a set of bits, measurements that are missing or equal to zero are considered as zeroes and all other measurements are considered as ones.

Usage

jaccard(mat)

Arguments

mat	a matrix of data, with samples in rows and features in columns

Value

the Jaccard index between non-zero/missing values in each pair of columns

Examples

mat = matrix(c(1, rep(0, 9), rep(1, 4), rep(0, 6)), ncol = 2)
jaccard(mat)
mat = cbind(mat, c(0, rep(1, 5), rep(0, 4)))

skinnider/dismay documentation built on May 6, 2019, 12:21 p.m.