parMIKD: Parallel Kernel Density Mutual Information Estimate

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

A function that computes the mutual information between all pairs of rows (or specified ones) of matrix counts using Kernel Density Estimate. It is a wrapper of the functions of the package GenKern.

Usage

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parMIKD(idx)

Arguments

idx

a numeric matrix (for the reconstruction of gene regulatory networks, genes on rows and samples on columns).

Details

Internal of parMIEstimate.

Value

The parMIKD function returns the value of the mutual information of that pair of genes I(X,Y).

Author(s)

Luciano Garofano [email protected], Stefano Maria Pagnotta, Michele Ceccarelli

References

Moon Y., Rajagopalan B., Lall U. (1995). Estimation of mutual information using kernel density estimators. Physical Review E, vol. 52 n. 3 pp. 2318-2321.

See Also

parEntropyEstimate, parMIEstimate

Examples

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simData <- simulatedData(p = 10, n = 50, mu = 100, sigma = 0.25,
                        ppower = 0.73, noise = FALSE)
counts <- simData$counts
adjMat <- simData$adjMat

miKD <- parMIEstimate(counts, method = "KD", nchips = 2)

lucgar/synRNASeqNet documentation built on May 21, 2019, 8:54 a.m.