# Empirical Bayesian analysis of patterns of differential expression in count data

## Documentation for package ‘baySeq’ version 2.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.
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.BB | 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
pairedData | baySeq - classes
pairedData-class | baySeq - classes
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