Empirical Bayesian analysis of patterns of differential expression in count data


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Documentation for package ‘baySeq’ version 1.0.0

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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
countData baySeq - classes
countData-class baySeq - classes
countDataPosterior baySeq - classes
countDataPosterior-class baySeq - classes
dim,countData-method baySeq - classes
dim,countDataPosterior-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.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
logsum An internal function for the baySeq package that calculates the log of the sum of the exponential of two variables
PDgivenr Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution.
PDgivenr.Dirichlet Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution.
PDgivenr.NBIndie Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution.
PDgivenr.Pois Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution.
PDgivenr.PoisIndie Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution.
show,countData-method baySeq - classes
show,countDataPosterior-method baySeq - classes
simCount Simulated data for testing the baySeq package methods; simulated counts from a pairwise differential expression analysis
topCounts Get the top counts corresponding to some group from a 'countDataPosterior' object
[,countData-method baySeq - classes
[,countDataPosterior-method baySeq - classes