entropyShrink: James-Stein Shrinkage Entropy Estimate

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

View source: R/entropyShrink.R

Description

Computing the James-Stein Shrinkage Entropy Estimate of cellCounts.

Usage

1
entropyShrink(cellCounts, unit = unit, shrinkageTarget = shrinkageTarget)

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).

shrinkageTarget

shrinkage target frequencies. If not specified (default) it is estimated in a James-Stein-type fashion (uniform distribution).

Value

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

Author(s)

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

References

James W., Stein C. (1961). Estimation with Quadratic Loss. Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability, vol. 1 pp. 361-379.

See Also

entropyML, entropyMM, entropyBayes, entropyCS

Examples

1
2
3
4
simData <- simulatedData(p = 50, n = 100, mu = 100, sigma = 0.25,
                        ppower = 0.73, noise = FALSE)
cellCounts <- table(simData$counts[1, ])
eShrink <- entropyShrink(cellCounts, unit = "nat", shrinkageTarget = NULL)

lucgar/synRNASeqNet documentation built on May 21, 2017, 3:39 p.m.