| 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"' |