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| baySeq-package | Empirical Bayesian analysis of patterns of differential expression in count data. |
| allModels | Function to generate all possible models for a countData object based on the replicate data. |
| baySeq | Empirical Bayesian analysis of patterns of differential expression in count data. |
| baySeq-class | baySeq - classes |
| baySeq-classes | baySeq - classes |
| bbDensity | Lists all currently available densityFunctions. |
| bbNCDist | Lists all currently available densityFunctions. |
| bimodalSeparator | A function that, given a numeric vector, finds the value which splits the data into two sets of minimal total variance using Otsu's method. |
| c-method | baySeq - classes |
| CDPost | 'countData' object derived from data file 'simData' with estimated likelihoods of differential expression. |
| CDPriors | 'countData' object derived from data file 'simData' with estimated priors. |
| countData | baySeq - classes |
| countData-class | baySeq - classes |
| densityFunction | baySeq - classes |
| densityFunction-class | Class '"densityFunction"' |
| densityFunction-method | baySeq - classes |
| densityFunction<- | baySeq - classes |
| densityFunction<--method | baySeq - classes |
| densityFunctions | Lists all currently available densityFunctions. |
| dim-method | baySeq - classes |
| getLibsizes | Estimates library scaling factors (library sizes) for count data. |
| getLikelihoods | Finds posterior likelihoods for each count or paired count as belonging to some model. |
| getLikelihoods.BB | Finds posterior likelihoods for each count or paired count as belonging to some model. |
| getLikelihoods.NB | Finds posterior likelihoods for each count or paired count as belonging to some model. |
| getPosteriors | An internal function in the baySeq package for calculating posterior likelihoods given likelihoods of the data. |
| getPriors | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.NB | Estimates prior parameters for the underlying distributions of 'count' data. |
| getTPs | Gets the number of true positives in the top n counts selected by ranked posterior likelihoods |
| groups | baySeq - classes |
| groups-method | baySeq - classes |
| groups<- | baySeq - classes |
| groups<--method | baySeq - classes |
| libsizes | baySeq - classes |
| libsizes-method | baySeq - classes |
| libsizes<- | baySeq - classes |
| libsizes<--method | baySeq - classes |
| makeOrderings | Construct orderings for count data given a model structure and an ordering function. |
| marginaliseEqual | Computes marginal likelihoods that two replicate groups are equal. |
| marginalisePairwise | Computes marginal likelihoods that two replicate groups differ, in a paticular direction. |
| md2Density | Lists all currently available densityFunctions. |
| md3Density | Lists all currently available densityFunctions. |
| mdDensity | Lists all currently available densityFunctions. |
| methObservables | Generation of intermediate values in likelihood estimation for methylation data. |
| mobAnnotation | Annotation data for a set of small RNA loci derived from sequencing of grafts of Arabidopsis thaliana intended for differential expression analyses. |
| mobData | Data from a set of small RNA sequencing experiments carried out on grafts of Arabidopsis thaliana intended for differential expression analyses. |
| nbinomDensity | Lists all currently available densityFunctions. |
| normDensity | Lists all currently available densityFunctions. |
| pairData | Simulated data for testing the baySeq package methods for paired data |
| plotMA.CD | 'MA'-plot for count data. |
| plotNullPrior | Plots distribution of null function and shows the threshold separator. |
| plotPosteriors | Plots the posterior likelihoods estimated for a 'countData' object against the log-ratios observed between two sets of sample data. |
| plotPriors | Plots the density of the log values estimated for the mean rate in the prior data for the Negative Binomial approach to detecting differential expression |
| rbind | baySeq - classes |
| rbind-method | baySeq - classes |
| replicates | baySeq - classes |
| replicates-method | baySeq - classes |
| replicates<- | baySeq - classes |
| replicates<--method | baySeq - classes |
| seglens | baySeq - classes |
| seglens-method | baySeq - classes |
| seglens<- | baySeq - classes |
| seglens<--method | baySeq - classes |
| selectTop | Selects the top genomic events, based on posterior likelihoods, from a 'countData' object. |
| show-method | baySeq - classes |
| simData | Simulated data for testing the baySeq package methods |
| summarisePosteriors | Summarises expected number of genomic events given the calculated posterior likelihoods of a countData object. |
| topCounts | Get the top counts corresponding to some group from a 'countData' object |
| zimData | Simulated data for testing the baySeq package methods |
| ZINBDensity | Lists all currently available densityFunctions. |
| [-method | baySeq - classes |