qsea-package	qsea-package
addCNV	addCNV
addContrast	addContrast
addCoverage	addCoverage
addEnrichmentParameters	addEnrichmentParameters
addLibraryFactors	addLibraryFactors
addNewSamples	addNewSamples
addOffset	addOffset
addParameters,qseaGLM-method	qseaGLM-class
addParameters,qseaSet-method	qseaSet-class
addPatternDensity	addPatternDensity
addSeqPref	addSeqPref
createQseaSet	createQseaSet
fitNBglm	fitNBglm
getChrNames	qseaSet-class
getChrNames,qseaSet-method	qseaSet-class
getCNV	qseaSet-class
getCNV,qseaSet-method	qseaSet-class
getCounts	qseaSet-class
getCounts,qseaSet-method	qseaSet-class
getExampleQseaSet	example
getLibSize	qseaSet-class
getLibSize,qseaSet-method	qseaSet-class
getNormFactors	qseaSet-class
getNormFactors,qseaSet-method	qseaSet-class
getOffset	qseaSet-class
getOffset,qseaSet-method	qseaSet-class
getParameters	qseaSet-class
getParameters,qseaGLM-method	qseaGLM-class
getParameters,qseaSet-method	qseaSet-class
getPCA	getPCA
getRegions	qseaSet-class
getRegions,qseaSet-method	qseaSet-class
getSampleGroups	qseaSet-class
getSampleGroups,qseaSet-method	qseaSet-class
getSampleNames	qseaSet-class
getSampleNames,qseaGLM-method	qseaGLM-class
getSampleNames,qseaPCA-method	qseaPCA-class
getSampleNames,qseaSet-method	qseaSet-class
getSampleTable	qseaSet-class
getSampleTable,qseaSet-method	qseaSet-class
getWindowSize	qseaSet-class
getWindowSize,qseaSet-method	qseaSet-class
getZygosity	qseaSet-class
getZygosity,qseaSet-method	qseaSet-class
hasCNV	qseaSet-class
hasCNV,qseaSet-method	qseaSet-class
isSignificant	isSignificant
makeTable	makeTable
normMethod	normMethod
plotCNV	plotCNV
plotCoverage	plotCoverage
plotEnrichmentProfile	plotEnrichmentProfile
plotEPmatrix	plotEnrichmentProfile
plotPCA	plotPCA
plotPCA,qseaPCA-method	plotPCA
plotPCAfactors	plotPCA
plotPCAfactors,qseaPCA-method	plotPCA
QSEA	qsea-package
qsea	qsea-package
qseaGLM	qseaGLM-class
qseaGLM-class	qseaGLM-class
qseaPCA	qseaPCA-class
qseaPCA-class	qseaPCA-class
qseaSet	qseaSet-class
qseaSet-class	qseaSet-class
regionStats	regionStats
setZygosity	qseaSet-class
setZygosity,qseaSet-method	qseaSet-class
show,qseaGLM-method	qseaGLM-class
show,qseaPCA-method	qseaPCA-class
show,qseaSet-method	qseaSet-class
