hamming: Calculate the Hamming distance between all columns in a...

In skinnider/dismay: dismay: distance metrics for matrices

Description

Calculate the Hamming distance between all pairs of columns in a matrix. The Hamming distance is defined as the number of positions in two vectors at which the corresponding symbols or different. Here, the Hamming distance is applied to the presence/absence of each gene, whereby measurements that are missing or equal to zero are considered as zeroes and all other measurements are considered as ones.

Usage

hamming(mat)

Arguments

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

Details

The matrix implementation used in dismay was obtained from: https://johanndejong.wordpress.com/2015/10/02/faster-hamming-distance-in-r-2/

Value

the Hamming 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)
hamming(mat)
mat = cbind(mat, c(0, rep(1, 5), rep(0, 4)))
hamming(mat)

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