parMIKD: Parallel Kernel Density Mutual Information Estimate
In synRNASeqNet: Synthetic RNA-Seq Network Generation and Mutual Information Estimates

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

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.

1	parMIKD(idx)

idx

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

Internal of parMIEstimate.

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

Luciano Garofano lucianogarofano88@gmail.com, Stefano Maria Pagnotta, Michele Ceccarelli

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.

parEntropyEstimate, parMIEstimate

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)