acceptanceRate	MixModelBayes-class
acceptanceRate,MixModelBayes-method	MixModelBayes-class
as.data.frame,MixModel-method	MixModel-class
bayesMixModel	bayesMixModel
bayesMixModel,numeric-method	bayesMixModel
calculateCrossCorrelation	calculateCrossCorrelation
calculateCrossCorrelation,GRanges-method	calculateCrossCorrelation
chains	MixModelBayes-class
chains,MixModelBayes-method	MixModelBayes-class
ChIPseqSet	ChIPseqSet-class
ChIPseqSet,matrix,GRanges-method	ChIPseqSet-class
ChIPseqSet,matrix,GRangesList-method	ChIPseqSet-class
ChIPseqSet-class	ChIPseqSet-class
chipVals	ChIPseqSet-class
chipVals,ChIPseqSet-method	ChIPseqSet-class
chipVals<-	ChIPseqSet-class
chipVals<-,ChIPseqSet,matrix-method	ChIPseqSet-class
classification	MixModel-class
classification,MixModel,character-method	MixModel-class
classification,MixModel,missing-method	MixModel-class
components	MixModel-class
components,MixModel-method	MixModel-class
convergence	MixModelML-class
convergence,MixModelML-method	MixModelML-class
cpm	ChIPseqSet-class
cpm,ChIPseqSet-method	ChIPseqSet-class
dim,MixModel-method	MixModel-class
eSet	eSet
fpkm	fpkm
getAlignmentQuality	getAlignmentQuality
getAlignmentQuality,character-method	getAlignmentQuality
integrateData	integrateData
integrateData,ExpressionSet,ChIPseqSet,character,character-method	integrateData
integrateData,ExpressionSet,ChIPseqSet,character,missing-method	integrateData
integrateData,ExpressionSetIllumina,ChIPseqSet,character,character-method	integrateData
integrateData,ExpressionSetIllumina,ChIPseqSet,character,missing-method	integrateData
length,MixModel-method	MixModel-class
listClassificationMethods	MixModel-class
listClassificationMethods,MixModel-method	MixModel-class
mappedReads	mappedReads
matchProbeToPromoter	matchProbeToPromoter
matchProbeToPromoter,list,data.frame-method	matchProbeToPromoter
MixModel-class	MixModel-class
MixModelBayes-class	MixModelBayes-class
MixModelML-class	MixModelML-class
MixtureComponent-class	MixtureComponent-class
mlMixModel	mlMixModel
mlMixModel,numeric-method	mlMixModel
mmData	MixModel-class
mmData,MixModel-method	MixModel-class
normalize	normalize
normalize,ChIPseqSet-method	normalize
normalize,ExpressionSet-method	normalize
normalizeChIP	normalizeChIP
normalizeChIP,ChIPseqSet,character-method	normalizeChIP
plotChains	plotChains
plotChains,MixModelBayes-method	plotChains
plotClassification	plotClassification
plotClassification,MixModel-method	plotClassification
plotComponents	plotComponents
plotComponents,MixModel-method	plotComponents
show,MixModel-method	MixModel-class
show,MixtureComponent-method	MixtureComponent-class
summarizeReads	summarizeReads
summarizeReads,GRangesList,GRanges,character-method	summarizeReads
summarizeReads,GRangesList,GRanges,missing-method	summarizeReads
summarizeReads,GRangesList,GRangesList,character-method	summarizeReads
summarizeReads,GRangesList,GRangesList,missing-method	summarizeReads
summary,MixModel-method	MixModel-class
summary,MixModelBayes-method	MixModel-class
transToTSS	transToTSS
weights,MixModel-method	MixModel-class
