Jensen-Shannon distance on columns

Description

JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a dist object of the pairwise Jensen-Shannon distances between columns

Usage

JSdist(mat,...)

Arguments

Details

Returns pairwise Jensen-Shannon distance (in the form of a dist object) for a matrix of probabilities (by column)

Value

A dist object of pairwise J-S distances between columns.

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

mat<-matrix(sample(1:50,50),10)
probs<-makeprobs(mat)
js.distance<-JSdist(probs)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(cummeRbund)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

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

    promoters

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

    promoters

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

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/JSdist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: JSdist
> ### Title: Jensen-Shannon distance on columns
> ### Aliases: JSdist
> ### Keywords: Jensen-Shannon distance metric JS
> 
> ### ** Examples
> 
> 
> mat<-matrix(sample(1:50,50),10)
> probs<-makeprobs(mat)
> js.distance<-JSdist(probs)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>