ChromosomeArmModels-class	ChromosomeArmModels-class
ChromosomeModels-class	ChromosomeModels-class
dependency score plotting	plot
DependencyModel-class	DependencyModel-class
findModel	ChromosomeArmModels-class
findModel,ChromosomeArmModels-method	ChromosomeArmModels-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
fit.dependency.model	fit.dependency.model
fixed.window	window
geneCopyNum	geneCopyNum
geneExp	geneExp
GenomeModels-class	GenomeModels-class
getArm	ChromosomeArmModels-class
getArm,ChromosomeArmModels-method	ChromosomeArmModels-class
getArm,DependencyModel-method	DependencyModel-class
getChromosome	ChromosomeArmModels-class
getChromosome,ChromosomeArmModels-method	ChromosomeArmModels-class
getChromosome,ChromosomeModels-method	ChromosomeModels-class
getChromosome,DependencyModel-method	DependencyModel-class
getGeneName	DependencyModel-class
getGeneName,ChromosomeArmModels-method	ChromosomeArmModels-class
getGeneName,DependencyModel-method	DependencyModel-class
getLoc	DependencyModel-class
getLoc,ChromosomeArmModels-method	ChromosomeArmModels-class
getLoc,DependencyModel-method	DependencyModel-class
getModelMethod	ChromosomeArmModels-class
getModelMethod,ChromosomeArmModels-method	ChromosomeArmModels-class
getModelMethod,ChromosomeModels-method	ChromosomeModels-class
getModelMethod,DependencyModel-method	DependencyModel-class
getModelMethod,GenomeModels-method	GenomeModels-class
getModelNumbers	ChromosomeArmModels-class
getModelNumbers,ChromosomeArmModels-method	ChromosomeArmModels-class
getParams	ChromosomeArmModels-class
getParams,ChromosomeArmModels-method	ChromosomeArmModels-class
getParams,ChromosomeModels-method	ChromosomeModels-class
getParams,DependencyModel-method	DependencyModel-class
getParams,GenomeModels-method	GenomeModels-class
getPArm	ChromosomeModels-class
getPArm,ChromosomeModels-method	ChromosomeModels-class
getPhi	DependencyModel-class
getPhi,DependencyModel-method	DependencyModel-class
getQArm	ChromosomeModels-class
getQArm,ChromosomeModels-method	ChromosomeModels-class
getScore	DependencyModel-class
getScore,ChromosomeArmModels-method	ChromosomeArmModels-class
getScore,DependencyModel-method	DependencyModel-class
getW	DependencyModel-class
getW,DependencyModel-method	DependencyModel-class
getWindowSize	ChromosomeArmModels-class
getWindowSize,ChromosomeArmModels-method	ChromosomeArmModels-class
getWindowSize,ChromosomeModels-method	ChromosomeModels-class
getWindowSize,DependencyModel-method	DependencyModel-class
getWindowSize,GenomeModels-method	GenomeModels-class
isEmpty	ChromosomeArmModels-class
isEmpty,ChromosomeArmModels-method	ChromosomeArmModels-class
isEmpty,ChromosomeModels-method	ChromosomeModels-class
iterative.window	window
orderGenes	ChromosomeArmModels-class
orderGenes,ChromosomeArmModels-method	ChromosomeArmModels-class
orderGenes,ChromosomeModels-method	ChromosomeModels-class
orderGenes,GenomeModels-method	GenomeModels-class
pcca	fit.dependency.model
pcca.isotropic	fit.dependency.model
pfa	fit.dependency.model
pint.data	pint.data
pint.match	pint.data
plot.ChromosomeArmModels	plot
plot.ChromosomeModels	plot
plot.DependencyModel	plot
plot.GenomeModels	plot
ppca	fit.dependency.model
screen.cgh.mir	screen
screen.cgh.mrna	screen
setArm<-	DependencyModel-class
setArm<-,DependencyModel-method	DependencyModel-class
setChromosome<-	DependencyModel-class
setChromosome<-,DependencyModel-method	DependencyModel-class
setGeneName<-	DependencyModel-class
setGeneName<-,DependencyModel-method	DependencyModel-class
setLoc<-	DependencyModel-class
setLoc<-,DependencyModel-method	DependencyModel-class
sparse.window	window
topGenes	ChromosomeArmModels-class
topGenes,ChromosomeArmModels-method	ChromosomeArmModels-class
topGenes,ChromosomeModels-method	ChromosomeModels-class
topGenes,GenomeModels-method	GenomeModels-class
topModels	ChromosomeArmModels-class
topModels,ChromosomeArmModels-method	ChromosomeArmModels-class
topModels,ChromosomeModels-method	ChromosomeModels-class
topModels,GenomeModels-method	GenomeModels-class
W.effects	z.expectation
z.effects	z.expectation
z.expectation	z.expectation
[[	ChromosomeArmModels-class
[[,ChromosomeArmModels-method	ChromosomeArmModels-class
[[,GenomeModels-method	GenomeModels-class
[[<-	ChromosomeArmModels-class
[[<-,ChromosomeArmModels-method	ChromosomeArmModels-class
[[<-,GenomeModels-method	GenomeModels-class
