# Epigenetic and gene transcription data normalization and integration with mixture models

## Documentation for package ‘epigenomix’ version 1.14.0

- 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"'