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 |
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 |
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 |
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 |