PoiClaClu-package {PoiClaClu}

Classification and clustering of RNA sequencing data using a Poisson model

Description

A simple approach for performing classification and clustering of samples for which RNA sequencing data is available. Based upon a simple Poisson model proposed by a number of authors (e.g. Marioni et al Genome Research 2008, Bullard et al BMC Bioinformatics 2010, and others).

Details

Package:	PoiClaClu
Type:	Package
Version:	1.0.2
Date:	2013-01-02
License:	GPL-2
LazyLoad:	yes

Author(s)

Daniela Witten

Maintainer: Daniela Witten <[e-mail]>

References

D. Witten (2011) Classification and clustering of sequencing data using a Poisson model. Annals of Applied Statistics 5(4): 2493-2518.

Examples

# Poisson clustering #
set.seed(1)
dat <- CountDataSet(n=20,p=100,sdsignal=.5,K=4,param=10)
dd <- PoissonDistance(dat$x, type="mle")
print(dd)
ColorDendrogram(hclust(dd$dd), y=dat$y)

# Poisson classification #
set.seed(1)
dat <- CountDataSet(n=20,p=100,sdsignal=.1,K=4,param=10)
out <- Classify(x=dat$x,y=dat$y,xte=dat$xte,rhos=c(0,5,10))
print(out)