Empirical Bayesian analysis of patterns of differential expression in count data


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Documentation for package ‘baySeq’ version 1.6.0

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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.
countData baySeq - classes
countData-class baySeq - classes
dim-method baySeq - classes
factCount Simulated data for testing the baySeq package methods; simulated counts from a factorial design differential expression analysis
factlibsizes Simulated data for testing the baySeq package methods; simulated library sizes from a pairwise differential expression analysis
getLikelihoods Finds posterior likelihoods for each count as belonging to some hypothesis.
getLikelihoods.Dirichlet Finds posterior likelihoods for each count as belonging to some hypothesis.
getLikelihoods.NB Finds posterior likelihoods for each count as belonging to some hypothesis.
getLikelihoods.NBboot Finds posterior likelihoods for each count as belonging to some hypothesis.
getLikelihoods.Pois Finds posterior likelihoods for each count as belonging to some hypothesis.
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.Dirichlet Estimates prior parameters for the underlying distributions of 'count' data.
getPriors.NB Estimates prior parameters for the underlying distributions of 'count' data.
getPriors.Pois 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
libsizes Simulated data for testing the baySeq package methods; simulated library sizes from a pairwise differential expression analysis
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
show-method baySeq - classes
simCount Simulated data for testing the baySeq package methods; simulated counts from a pairwise differential expression analysis
simSeg Simulated data for testing the baySeq package methods; simulated counts and segment lengths from a pairwise differential expression analysis
topCounts Get the top counts corresponding to some group from a 'countData' object
[-method baySeq - classes