getDeps: Compute dependencies between positions

Description Usage Arguments Value Author(s) Examples

View source: R/DepLogoR.R

Description

Computes the dependencies (as measures by mutual information) between all positions (columns) of discrete data. Specifically, it returns for each pair of positions (i,j) the mutual information I(X_i,X_j) multiplied by the number N of sequences (rows), which may also be used for testing the statistical significance of mutual information values, as for large N, 2*N*I(X_i,X_j) is approximately chi squared.

Usage

1

Arguments

data

the data for computing mutual information. Either a DLData object or a data.frame; In the latter case, the symbols of the alphabet must be provided as a second parameter

...

the symbols of the alphabet as character vector, only if data is a data.frame

Value

a matrix of the mutual information values, where the diagonal is fixed to zero

Author(s)

Jan Grau <grau@informatik.uni-halle.de>

Examples

1
2
data <- DLData(c("ACGT", "ATTA"))
deps <- getDeps(data)

Jstacs/DepLogo documentation built on April 22, 2021, 1:21 a.m.