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 |