| allModels | Function to generate all possible models for a countData... |
| baySeq-classes | baySeq - classes |
| baySeq-package | Empirical Bayesian analysis of patterns of differential... |
| bimodalSep | A function that, given a numeric vector, finds the value... |
| CDPost | 'countData' object derived from data file 'simData' with... |
| CDPriors | 'countData' object derived from data file 'simData' with... |
| densityFunction | Class '"densityFunction"' |
| densityFunctions | Lists all currently available densityFunctions. |
| getLibsizes | Estimates library scaling factors (library sizes) for count... |
| getLikelihoods | Finds posterior likelihoods for each count or paired count as... |
| getPosteriors | An internal function in the baySeq package for calculating... |
| getPriors | Estimates prior parameters for the underlying distributions... |
| getTPs | Gets the number of true positives in the top n counts... |
| makeOrderings | Construct orderings for count data given a model structure... |
| marginaliseEqual | Computes marginal likelihoods that two replicate groups are... |
| marginalisePairwise | Computes marginal likelihoods that two replicate groups... |
| methObservables | Generation of intermediate values in likelihood estimation... |
| mobAnnotation | Annotation data for a set of small RNA loci derived from... |
| mobData | Data from a set of small RNA sequencing experiments carried... |
| pairData | Simulated data for testing the baySeq package methods for... |
| plotMA.CD | 'MA'-plot for count data. |
| plotNullPrior | Plots distribution of null function and shows the threshold... |
| plotPosteriors | Plots the posterior likelihoods estimated for a 'countData'... |
| plotPriors | Plots the density of the log values estimated for the mean... |
| selectTop | Selects the top genomic events, based on posterior... |
| simData | Simulated data for testing the baySeq package methods |
| summarisePosteriors | Summarises expected number of genomic events given the... |
| topCounts | Get the top counts corresponding to some group from a... |
| zimData | Simulated data for testing the baySeq package methods |
