Empirical Bayesian analysis of patterns of differential expression in count data


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Documentation for package ‘baySeq’ version 1.4.0

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baySeq-package Empirical Bayesian analysis of patterns of differential expression in
baySeq Empirical Bayesian analysis of patterns of differential expression in
baySeq-class baySeq - classes
baySeq-classes baySeq - classes
countData baySeq - classes
countData-class baySeq - classes
dim-method baySeq - classes
factCount Simulated data for testing the baySeq package methods; simulated counts
factlibsizes Simulated data for testing the baySeq package methods; simulated
getLikelihoods Finds posterior likelihoods for each count as belonging to some
getLikelihoods.Dirichlet Finds posterior likelihoods for each count as belonging to some
getLikelihoods.NB Finds posterior likelihoods for each count as belonging to some
getLikelihoods.NBboot Finds posterior likelihoods for each count as belonging to some
getLikelihoods.Pois Finds posterior likelihoods for each count as belonging to some
getPosteriors An internal function in the baySeq package for calculating posterior
getPriors Estimates prior parameters for the underlying distributions of 'count'
getPriors.Dirichlet Estimates prior parameters for the underlying distributions of 'count'
getPriors.NB Estimates prior parameters for the underlying distributions of 'count'
getPriors.Pois Estimates prior parameters for the underlying distributions of 'count'
getTPs Gets the number of true positives in the top n counts selected by
libsizes Simulated data for testing the baySeq package methods; simulated
plotMA.CD 'MA'-plot for count data.
plotPosteriors Plots the posterior likelihoods estimated for a 'countData' object
plotPriors Plots the density of the log values estimated for the mean rate in the
show-method baySeq - classes
simCount Simulated data for testing the baySeq package methods; simulated counts
simSeg Simulated data for testing the baySeq package methods; simulated counts
topCounts Get the top counts corresponding to some group from a 'countData'
[-method baySeq - classes