Empirical Bayesian analysis of patterns of differential expression in count data


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Documentation for package ‘baySeq’ version 2.2.0

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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.
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.
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