Epigenetic and gene transcription data normalization and integration with mixture models


[Up] [Top]

Documentation for package ‘epigenomix’ version 1.24.0

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"'