hdEntropy: Entropy estimation.

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

The (differential) entropy of a high-dimensional multivariate random variable is estimated from a (high-dimensional matrix) under a normality or k-NN distributional assumption.

Usage

hdEntropy(Y, method = "normal", k = 1, center = TRUE, indKnn = TRUE)

Arguments

Y	(High-dimensional) matrix. Rows are assumed to represent the samples, and columns represent the samples' genes or traits.
method	Distributional assumption under which entropy is to be estimated.
k	k-nearest neighbor parameter.
center	Logical indicator: should the columns of Y be centered around zero?
indKnn	Logical indicator: should samples' individual contributions to the k-NN entropy be reported?

Value

The entropy estimate is returned as a numeric.

Author(s)

Wessel N. van Wieringen: [e-mail]

References

Van Wieringen, W.N., Van der Vaart, A.W. (2011), "Statistical analysis of the cancer cell's molecular entropy using high-throughput data", Bioinformatics, 27(4), 556-563.

See Also

entropyTest.

Examples

data(pollackGE16)
hdEntropy(t(exprs(pollackGE16)), method="knn")

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: mvtnorm
 [1] 265.0875 314.8138 341.9452 265.0875 255.8793 236.1673 240.3278 268.4733
 [9] 235.3109 218.0154 208.1410 223.4255 261.5972 239.5631 230.2853 223.2162
[17] 213.6865 259.9325 204.6118 230.8339 204.6118 229.1563 242.2085 190.0908
[25] 190.0908 196.4310 235.5555 240.3278 272.7666 218.0759 238.1410 195.7186
[33] 205.7374 309.7156 257.9855 241.4646 229.9581 261.5972 165.6367 165.6367
[41] 202.8282

sigaR documentation built on April 28, 2020, 6:05 p.m.