Epigenetic and gene transcription data normalization and integration with mixture models

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Documentation for package ‘epigenomix’ version 1.47.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

acceptanceRate	Class '"MixModelBayes"'
acceptanceRate-method	Class '"MixModelBayes"'
as.data.frame-method	Class '"MixModel"'
bayesMixModel	Fits a Bayesian mixture model using Markov Chain Monte Carlo (MCMC) methods
bayesMixModel-method	Fits a Bayesian mixture model using Markov Chain Monte Carlo (MCMC) methods
calculateCrossCorrelation	Calculate the cross correlation for a given GRanges object.
calculateCrossCorrelation-method	Calculate the cross correlation for a given GRanges object.
chains	Class '"MixModelBayes"'
chains-method	Class '"MixModelBayes"'
ChIPseqSet	Class '"ChIPseqSet"'
ChIPseqSet-class	Class '"ChIPseqSet"'
ChIPseqSet-method	Class '"ChIPseqSet"'
chipVals	Class '"ChIPseqSet"'
chipVals-method	Class '"ChIPseqSet"'
chipVals<-	Class '"ChIPseqSet"'
chipVals<--method	Class '"ChIPseqSet"'
classification	Class '"MixModel"'
classification-method	Class '"MixModel"'
components	Class '"MixModel"'
components-method	Class '"MixModel"'
convergence	Class '"MixModelML"'
convergence-method	Class '"MixModelML"'
cpm	Class '"ChIPseqSet"'
cpm-method	Class '"ChIPseqSet"'
dim-method	Class '"MixModel"'
eSet	Example gene expression data set.
fpkm	Example RNA-seq data set.
getAlignmentQuality	Calculation of basic alignments statistics
getAlignmentQuality-method	Calculation of basic alignments statistics
integrateData	Calculates a normalized correlation score from ChIP-seq and microarray gene expression data.
integrateData-method	Calculates a normalized correlation score from ChIP-seq and microarray gene expression data.
length-method	Class '"MixModel"'
listClassificationMethods	Class '"MixModel"'
listClassificationMethods-method	Class '"MixModel"'
mappedReads	Mapped reads obtained from a anti-histone ChIP-seq experiment.
matchProbeToPromoter	A function assigning promoter regions to given probe IDs.
matchProbeToPromoter-method	A function assigning promoter regions to given probe IDs.
MixModel-class	Class '"MixModel"'
MixModelBayes-class	Class '"MixModelBayes"'
MixModelML-class	Class '"MixModelML"'
MixtureComponent-class	Class '"MixtureComponent"'
mlMixModel	Fits a mixture model using the maximum likelihood principle.
mlMixModel-method	Fits a mixture model using the maximum likelihood principle.
mmData	Class '"MixModel"'
mmData-method	Class '"MixModel"'
normalize	Normalization of ChIP-seq and other count data
normalize-method	Normalization of ChIP-seq and other count data
normalizeChIP	Normalization of ChIP-seq count data. (deprecated)
normalizeChIP-method	Normalization of ChIP-seq count data. (deprecated)
plotChains	Produces trace plots for a Bayesian mixture model
plotChains-method	Produces trace plots for a Bayesian mixture model
plotClassification	Plot classification obtained from a mixture model.
plotClassification-method	Plot classification obtained from a mixture model.
plotComponents	Plots the mixture density together with the densities of all single components.
plotComponents-method	Plots the mixture density together with the densities of all single components.
show-method	Class '"MixModel"'
show-method	Class '"MixtureComponent"'
summarizeReads	Count reads lying within given regions.
summarizeReads-method	Count reads lying within given regions.
summary-method	Class '"MixModel"'
transToTSS	A data frame with Ensemble transcript IDs and transcriptional start sites.
weights-method	Class '"MixModel"'