KLdist.matrix {bioDist}R Documentation

Discrete version of Kullback-Leibler Distance (KLD)

Description

Calculate the KLD by binning continuous data.

Usage

KLdist.matrix(x, ...)

Arguments

x n by p matrix or ExpressionSet; if x is an ExpressionSet,then the values returned by the exprs function are used.
... arguments passed to KLdist.matrix:
nbin
number of bins to calculate discrete probabilities; default is 10.
symmetrize
if TRUE, then symmetrize; default is FALSE.
diag
if TRUE, then the diagonal of the distance matrix will be displayed; default is FALSE.
upper
if TRUE, then the upper triangle of the distance matrix will be displayed; default is FALSE.
sample
for ExpressionSet methods: if TRUE, then the distances are computed between samples, otherwise, between genes.

Details

The data are binned, and then the KL distance between the two discrete distributions is computed and used.

The list method is meant for use when samples sizes are unequal.

Value

Pairwsie KLD object

Author(s)

Beiying Ding

See Also

cor.dist, spearman.dist, tau.dist,euc, man,KLD.matrix,mutualInfo

Examples

 x <- matrix(rnorm(100), nrow = 5)
 KLdist.matrix(x, symmetrize = TRUE, nbin = 3) 

[Package bioDist version 1.14.0 Index]