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 |