as.data.frame,ChromosomeModels-method	ChromosomeModels-class
as.data.frame,GenomeModels-method	GenomeModels-class
ChromosomeModels-class	ChromosomeModels-class
dependency score plotting	plot
findModel	ChromosomeModels-class
findModel,ChromosomeModels-method	ChromosomeModels-class
findModel,GenomeModels-method	GenomeModels-class
fit.byname	fit.byname
fit.cgh.mir.byname	fit.byname
fit.cgh.mrna.byname	fit.byname
fixed.window	window
geneCopyNum	geneCopyNum
GeneDependencyModel-class	GeneDependencyModel-class
geneExp	geneExp
GenomeModels-class	GenomeModels-class
get.neighboring.probes	get.neighboring.probes
get.neighs	get.neighs
getArm	ChromosomeModels-class
getArm,ChromosomeModels-method	ChromosomeModels-class
getArm,GeneDependencyModel-method	GeneDependencyModel-class
getChromosome	ChromosomeModels-class
getChromosome,ChromosomeModels-method	ChromosomeModels-class
getChromosome,GeneDependencyModel-method	GeneDependencyModel-class
getGeneName	ChromosomeModels-class
getGeneName,ChromosomeModels-method	ChromosomeModels-class
getGeneName,GeneDependencyModel-method	GeneDependencyModel-class
getLoc	GeneDependencyModel-class
getLoc,ChromosomeModels-method	ChromosomeModels-class
getLoc,GeneDependencyModel-method	GeneDependencyModel-class
getModelMethod	ChromosomeModels-class
getModelMethod,ChromosomeModels-method	ChromosomeModels-class
getModelMethod,GenomeModels-method	GenomeModels-class
getModelNumbers	ChromosomeModels-class
getModelNumbers,ChromosomeModels-method	ChromosomeModels-class
getModelNumbers,GenomeModels-method	GenomeModels-class
getParams	ChromosomeModels-class
getParams,ChromosomeModels-method	ChromosomeModels-class
getParams,GenomeModels-method	GenomeModels-class
getPArm	ChromosomeModels-class
getPArm,ChromosomeModels-method	ChromosomeModels-class
getQArm	ChromosomeModels-class
getQArm,ChromosomeModels-method	ChromosomeModels-class
getScore	GeneDependencyModel-class
getScore,ChromosomeModels-method	ChromosomeModels-class
getScore,GeneDependencyModel-method	GeneDependencyModel-class
getWindowSize	ChromosomeModels-class
getWindowSize,ChromosomeModels-method	ChromosomeModels-class
getWindowSize,GeneDependencyModel-method	GeneDependencyModel-class
getWindowSize,GenomeModels-method	GenomeModels-class
getZ,GeneDependencyModel-method	GeneDependencyModel-class
isEmpty	ChromosomeModels-class
isEmpty,ChromosomeModels-method	ChromosomeModels-class
iterative.window	window
join.top.regions	join.top.regions
order.feature.info	order.feature.info
orderGenes	ChromosomeModels-class
orderGenes,ChromosomeModels-method	ChromosomeModels-class
orderGenes,GenomeModels-method	GenomeModels-class
pint.data	pint.data
pint.match	pint.data
plot.ChromosomeModels	plot
plot.GeneDependencyModel	plot
plot.GenomeModels	plot
screen.cgh.mir	screen
screen.cgh.mrna	screen
setArm<-	GeneDependencyModel-class
setArm<-,GeneDependencyModel-method	GeneDependencyModel-class
setChromosome<-	GeneDependencyModel-class
setChromosome<-,GeneDependencyModel-method	GeneDependencyModel-class
setGeneName<-	GeneDependencyModel-class
setGeneName<-,GeneDependencyModel-method	GeneDependencyModel-class
setLoc<-	GeneDependencyModel-class
setLoc<-,GeneDependencyModel-method	GeneDependencyModel-class
sparse.window	window
summarize.region.parameters	summarize.region.parameters
topGenes	ChromosomeModels-class
topGenes,ChromosomeModels-method	ChromosomeModels-class
topGenes,GenomeModels-method	GenomeModels-class
topModels	ChromosomeModels-class
topModels,ChromosomeModels-method	ChromosomeModels-class
topModels,GenomeModels-method	GenomeModels-class
W.effects	z.effect
z.effects	z.effect
[[	ChromosomeModels-class
[[,ChromosomeModels-method	ChromosomeModels-class
[[,GenomeModels-method	GenomeModels-class
[[<-	ChromosomeModels-class
[[<-,ChromosomeModels-method	ChromosomeModels-class
[[<-,GenomeModels-method	GenomeModels-class
