entropy: Shannon entropy

In BioQC: Detect tissue heterogeneity in expression profiles with gene sets

Description

Shannon entropy

Usage

entropy(vector)

Arguments

vector

A vector of numbers, or characters. Discrete probability of each item is calculated and the Shannon entropy is returned.

Value

Shannon entropy

Shannon entropy can be used as measures of gene expression specificity, as well as measures of tissue diversity and specialization. See references below.

We use 2 as base for the entropy calculation, because in this base the unit of entropy is bit.

Author(s)

Jitao David Zhang <[e-mail]>

References

Martinez and Reyes-Valdes (2008) Defining diversity, specialization, and gene specificity in transcriptomes through information theory. PNAS 105(28):9709–9714

Examples

myVec0 <- 1:9
entropy(myVec0) ## log2(9)
myVec1 <- rep(1, 9)
entropy(myVec1)

entropy(LETTERS)
entropy(rep(LETTERS, 5))

Example output

Loading required package: Rcpp
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")'.

[1] 3.169925
[1] 0
[1] 4.70044
[1] 4.70044

BioQC documentation built on Nov. 8, 2020, 7:16 p.m.