dist2: Calculate an n-by-n matrix by applying a function to all...

In Bioconductor/genefilter: genefilter: methods for filtering genes from high-throughput experiments

Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix.

Description

Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix.

Usage

  dist2(x, fun, diagonal=0)

Arguments

x	A matrix.
fun	A symmetric function of two arguments that may be columns of x.
diagonal	The value to be used for the diagonal elements of the resulting matrix.

Details

With the default value of fun, this function calculates for each pair of columns of x the mean of the absolute values of their differences (which is proportional to the L1-norm of their difference). This is a distance metric.

The implementation assumes that fun(x[,i], x[,j]) can be evaluated for all pairs of i and j (see examples), and that fun is symmetric, i.e. fun(a, b) = fun(b, a). fun(a, a) is not actually evaluated, instead the value of diagonal is used to fill the diagonal elements of the returned matrix.

Note that dist computes distances between rows of x, while this function computes relations between columns of x (see examples).

Value

A symmetric matrix of size n x n.

Author(s)

Wolfgang Huber, James Reid

Examples

  # example matrix
  z = matrix(1:15693, ncol=3)
  matL1 = dist2(z)
  matL2 = dist2(z, fun=function(a,b) sqrt(sum((a-b)^2, na.rm=TRUE)))

  euc = as.matrix(dist(t(z)))

  stopifnot(identical(dim(matL2), dim(euc)),
            all(euc==matL2))

Bioconductor/genefilter documentation built on Feb. 4, 2024, 11:20 a.m.