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

Global functions
.bayesMixModel Source code
.calculateCrossCorrelation Source code
.getAlignmentQuality Source code
.integrateData Source code
.matchProbeToPromoter Source code
.mlMixModel Source code
.normalize Source code
.normalize.quantile Source code
.normalize.scale Source code
.normalize.scaleMedianRegion Source code
.normalize.tmm Source code
.normalizeChIP Source code
.plotChains Source code
.plotClassification Source code
.plotComponents Source code
.sampleAllocations Source code
.sampleAlpha Source code
.sampleComponentParameters Source code
.sampleMixture Source code
.sampleMixtureTDP Source code
.sampleShape Source code
.summarizeReads Source code
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
bayesMixModel,numeric-method Man page
calculateCrossCorrelation Man page
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
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
matchProbeToPromoter,list,data.frame-method Man page
mlMixModel Man page
mlMixModel,numeric-method Man page
mmData Man page
mmData,MixModel-method Man page
normalize Man page
normalize,ChIPseqSet-method Man page
normalize,ExpressionSet-method Man page
normalizeChIP Man page
normalizeChIP,ChIPseqSet,character-method Man page
plotChains Man page
plotChains,MixModelBayes-method Man page
plotClassification Man page
plotClassification,MixModel-method Man page
plotComponents Man page
plotComponents,MixModel-method Man page
show,MixModel-method Man page
show,MixtureComponent-method Man page
summarizeReads Man page
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 April 29, 2020, 6:30 a.m.