API for epigenomix
Epigenetic and gene transcription data normalization and integration with mixture models

Global functions
ChIPseqSet Man page
ChIPseqSet,matrix,GRanges-method Man page
ChIPseqSet,matrix,GRangesList-method Man page
ChIPseqSet-class Man page
MixModel-class Man page
MixModelBayes-class Man page
MixModelML-class Man page
MixtureComponent-class Man page
acceptanceRate Man page
acceptanceRate,MixModelBayes-method Man page
as.data.frame,MixModel-method Man page
bayesMixModel Man page Source code
bayesMixModel,numeric-method Man page
calculateCrossCorrelation Man page Source code
calculateCrossCorrelation,GRanges-method Man page
chains Man page
chains,MixModelBayes-method Man page
chipVals Man page
chipVals,ChIPseqSet-method Man page
chipVals<- Man page
chipVals<-,ChIPseqSet,matrix-method Man page
classification Man page
classification,MixModel,character-method Man page
classification,MixModel,missing-method Man page
components Man page
components,MixModel-method Man page
convergence Man page
convergence,MixModelML-method Man page
cpm Man page
cpm,ChIPseqSet-method Man page
dim,MixModel-method Man page
eSet Man page
fpkm Man page
getAlignmentQuality Man page Source code
getAlignmentQuality,character-method Man page
integrateData Man page
integrateData,ExpressionSet,ChIPseqSet,character,character-metho Man page
integrateData,ExpressionSet,ChIPseqSet,character,missing-method Man page
integrateData,ExpressionSetIllumina,ChIPseqSet,character,charact Man page
integrateData,ExpressionSetIllumina,ChIPseqSet,character,missing Man page
length,MixModel-method Man page
listClassificationMethods Man page
listClassificationMethods,MixModel-method Man page
mappedReads Man page
matchProbeToPromoter Man page Source code
matchProbeToPromoter,list,data.frame-method Man page
mlMixModel Man page Source code
mlMixModel,numeric-method Man page
mmData Man page
mmData,MixModel-method Man page
normalize Man page Source code
normalize,ChIPseqSet-method Man page
normalize,ExpressionSet-method Man page
normalize.quantile Source code
normalize.scale Source code
normalize.scaleMedianRegion Source code
normalize.tmm Source code
normalizeChIP Man page Source code
normalizeChIP,ChIPseqSet,character-method Man page
ntegrateData Source code
plotChains Man page Source code
plotChains,MixModelBayes-method Man page
plotClassification Man page Source code
plotClassification,MixModel-method Man page
plotComponents Man page Source code
plotComponents,MixModel-method Man page
sampleAllocations Source code
sampleAlpha Source code
sampleComponentParameters Source code
sampleMixture Source code
sampleMixtureTDP Source code
sampleShape Source code
show,MixModel-method Man page
show,MixtureComponent-method Man page
summarizeReads Man page Source code
summarizeReads,GRangesList,GRanges,character-method Man page
summarizeReads,GRangesList,GRanges,missing-method Man page
summarizeReads,GRangesList,GRangesList,character-method Man page
summarizeReads,GRangesList,GRangesList,missing-method Man page
summary,MixModel-method Man page
summary,MixModelBayes-method Man page
transToTSS Man page
weights,MixModel-method Man page
epigenomix documentation built on Nov. 1, 2018, 3:57 a.m.