getDeps {DepLogo}

Compute dependencies between positions

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

getDeps(data, ...)

## S3 method for class 'DLData'
getDeps(data, ...)

## S3 method for class 'data.frame'
getDeps(data, alphabet, ...)

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

alphabet

only required when called on a data.frame

Value

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

Author(s)

Jan Grau <[e-mail]>

Examples

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