entropyBayes: Bayesian Entropy Estimate

In synRNASeqNet: Synthetic RNA-Seq Network Generation and Mutual Information Estimates

Description

Computing the Maximul Likelihood Entropy Estimate of cellCounts.

Usage

entropyBayes(cellCounts, unit = unit,
            priorHyperParam = priorHyperParam)

Arguments

cellCounts	an integer vector (or matrix) representing the number of times each particular count is obtained.
unit	the unit in which entropy is measured. One of "bit" (log2, default), "ban" (log10) or "nat" (natural units).
priorHyperParam	the prior distribution type for the Bayes estimation. One of "Jeffreys" (default, Jeffreys Prior, Krichevsky and Trofimov Estimator), "BLUnif" (Bayes-Laplace uniform Prior, Holste Estimator), "Perks" (Perks Prior, Schurmann and Grassberger Estimator), or "MiniMax" (MiniMax Prior), can be abbreviated.

Value

The entropyBayes function returns the value of the entropy of that gene H(X) (or pair of genes H(X,Y)).

Author(s)

Luciano Garofano [e-mail], Stefano Maria Pagnotta, Michele Ceccarelli

References

Jeffreys H. (1946). An invariant form for the prior probability in estimation problems. Proceedings of the Royal Society of London, vol. 186 no. 1007 pp. 453-461.

Krichevsky R.E., Trofimov V.K. (1981). The performance of universal encoding. IEEE Transactions on Information Theory, vol. 27 pp. 199-207.

Holste D., Hertzel H. (1998). Bayes' estimators of generalized entropies. Journal of Physics A, vol. 31 pp. 2551-2566.

Perks W. (1947). Some observations on inverse probability including a new indifference rule. Journal of the Institute of Actuaries, vol. 73 pp. 285-334.

Schurmann T., Grassberg P. (1996). Entropy estimation of symbol sequences. Chaos, vol. 6 pp. 414-427.

Trybula S. (1958). Some problems of simultaneous minimax estimation. The Annals of Mathematical Statistics, vol. 29 pp. 245-253.

See Also

entropyML, entropyMM, entropyCS, entropyShrink

Examples

simData <- simulatedData(p = 50, n = 100, mu = 100, sigma = 0.25,
                        ppower = 0.73, noise = FALSE)
cellCounts <- table(simData$counts[1, ])
eBJ <- entropyBayes(cellCounts, unit = "nat", priorHyperParam = "Jeffreys")
eBB <- entropyBayes(cellCounts, unit = "nat", priorHyperParam = "BLUnif")
eBP <- entropyBayes(cellCounts, unit = "nat", priorHyperParam = "Perks")
eBM <- entropyBayes(cellCounts, unit = "nat", priorHyperParam = "MiniMax")

Example output

Loading required package: parallel
Loading required package: parmigene
Loading required package: GenKern
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

synRNASeqNet documentation built on May 2, 2019, 6:01 a.m.