entropySpecificity: Entropy-based gene-expression specificity

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

Description

Entropy-based gene-expression specificity

Usage

entropySpecificity(mat, norm = FALSE)

Arguments

mat	A matrix (usually an expression matrix), with genes (features) in rows and samples in columns.
norm	Logical, whether the specificity should be normalized by log2(ncol(mat)).

Value

A vector of the length of the row number of the input matrix, namely the specificity score of genes.

References

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

See Also

entropy

Examples

myMat <- rbind(c(3,4,5),c(6,6,6), c(0,2,4))
entropySpecificity(myMat)
entropySpecificity(myMat, norm=TRUE)

myRandomMat <- matrix(runif(1000), ncol=20)
entropySpecificity(myRandomMat)
entropySpecificity(myRandomMat, norm=TRUE)

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] 0.00000000 0.03168154 0.62372590
[1] 0.00000000 0.01998883 0.39352723
 [1] 0.32600543 0.15593379 0.21966140 0.20232590 0.27140945 0.15060209
 [7] 0.11245793 0.23091720 0.22957248 0.37475457 0.23288034 0.34379778
[13] 0.23390876 0.06527179 0.14618984 0.29268905 0.20634617 0.28276754
[19] 0.41989382 0.28328403 0.27493503 0.24325704 0.45964467 0.28182349
[25] 0.26117046 0.14043888 0.14049591 0.30461773 0.27733438 0.32131088
[31] 0.39383099 0.26164675 0.31423576 0.18851495 0.34512948 0.15522245
[37] 0.37354283 0.41475756 0.25658503 0.34672756 0.32147178 0.28975121
[43] 0.16748182 0.19359266 0.38968243 0.28555682 0.29806595 0.27129905
[49] 0.29161316 0.28967380
 [1] 0.07543055 0.03607968 0.05082486 0.04681380 0.06279823 0.03484604
 [7] 0.02602031 0.05342921 0.05311807 0.08671004 0.05388344 0.07954732
[13] 0.05412139 0.01510247 0.03382514 0.06772187 0.04774401 0.06542625
[19] 0.09715428 0.06554575 0.06361398 0.05628438 0.10635176 0.06520781
[25] 0.06042915 0.03249450 0.03250769 0.07048191 0.06416913 0.07434434
[31] 0.09112391 0.06053936 0.07270731 0.04361825 0.07985544 0.03591509
[37] 0.08642967 0.09596586 0.05936818 0.08022520 0.07438157 0.06704212
[43] 0.03875165 0.04479312 0.09016403 0.06607163 0.06896597 0.06277269
[49] 0.06747293 0.06702421

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