R: Jensen-Shannon distance on rows from a pre-defined vector of...
JSdistFromP
R Documentation
Jensen-Shannon distance on rows from a pre-defined vector of probabilities
Description
JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a matrix of Jensen-Shannon distances between individual rows
and a specific vector of probabilities (q)
Usage
JSdistFromP(mat,q)
Arguments
mat
A matrix of expression probabilities (e.g. from makeprobs())
q
A vector of expression probabilities.
Details
Returns Jensen-Shannon distance for each row of a matrix of probabilities against a provided probability distribution (q)
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/JSdistFromP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: JSdistFromP
> ### Title: Jensen-Shannon distance on rows from a pre-defined vector of
> ### probabilities
> ### Aliases: JSdistFromP
> ### Keywords: Jensen-Shannon distance metric JS
>
> ### ** Examples
>
>
> mat<-matrix(sample(1:50,50),10)
> q<-c(100,4,72,8,19)
> q<-q/sum(q)
> js.distance<-JSdistFromP(mat,q)
>
>
>
>
>
>
> dev.off()
null device
1
>