Empirical Bayesian analysis of patterns of differential expression in count data


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Documentation for package ‘baySeq’ version 1.12.0

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baySeq-package Empirical Bayesian analysis of patterns of differential expression in count data.
baySeq Empirical Bayesian analysis of patterns of differential expression in count data.
baySeq-class baySeq - classes
baySeq-classes baySeq - classes
bimodalSep A function that, given a numeric vector, finds the value which splits the data into two sets of minimal total variance.
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
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
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.
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.
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
show-method baySeq - classes
simData Simulated data for testing the baySeq package methods
topCounts Get the top counts corresponding to some group from a 'countData' object
[-method baySeq - classes