getDeps | R Documentation |
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.
getDeps(data, ...)
## S3 method for class 'DLData'
getDeps(data, ...)
## S3 method for class 'data.frame'
getDeps(data, alphabet, ...)
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 |
a matrix of the mutual information values, where the diagonal is fixed to zero
Jan Grau <grau@informatik.uni-halle.de>
data <- DLData(c("ACGT", "ATTA"))
deps <- getDeps(data)
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