baySeq-package |
Empirical Bayesian analysis of patterns of differential expression in count data. |
allModels |
Function to generate all possible models for a countData object based on the replicate data. |
baySeq |
Empirical Bayesian analysis of patterns of differential expression in count data. |
baySeq-class |
baySeq - classes |
baySeq-classes |
baySeq - classes |
bbDensity |
Lists all currently available densityFunctions. |
bbNCDist |
Lists all currently available densityFunctions. |
bimodalSeparator |
A function that, given a numeric vector, finds the value which splits the data into two sets of minimal total variance using Otsu's method. |
CDPost |
'countData' object derived from data file 'simData' with estimated likelihoods of differential expression. |
CDPriors |
'countData' object derived from data file 'simData' with estimated priors. |
countData |
baySeq - classes |
countData-class |
baySeq - classes |
densityFunction |
baySeq - classes |
densityFunction-class |
Class '"densityFunction"' |
densityFunction-method |
baySeq - classes |
densityFunction<- |
baySeq - classes |
densityFunction<--method |
baySeq - classes |
densityFunctions |
Lists all currently available densityFunctions. |
dim-method |
baySeq - classes |
getLibsizes |
Estimates library scaling factors (library sizes) for count data. |
getLikelihoods |
Finds posterior likelihoods for each count or paired count as belonging to some model. |
getLikelihoods.BB |
Finds posterior likelihoods for each count or paired count as belonging to some model. |
getLikelihoods.NB |
Finds posterior likelihoods for each count or paired count as belonging to some model. |
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.BB |
Estimates prior parameters for the underlying distributions of 'count' data. |
getPriors.NB |
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 |
groups |
baySeq - classes |
groups-method |
baySeq - classes |
groups<- |
baySeq - classes |
groups<--method |
baySeq - classes |
libsizes |
baySeq - classes |
libsizes-method |
baySeq - classes |
libsizes<- |
baySeq - classes |
libsizes<--method |
baySeq - classes |
makeOrderings |
Construct orderings for count data given a model structure and an ordering function. |
md2Density |
Lists all currently available densityFunctions. |
md3Density |
Lists all currently available densityFunctions. |
mdDensity |
Lists all currently available densityFunctions. |
methObservables |
Generation of intermediate values in likelihood estimation for methylation data. |
mobAnnotation |
Annotation data for a set of small RNA loci derived from sequencing of grafts of Arabidopsis thaliana intended for differential expression analyses. |
mobData |
Data from a set of small RNA sequencing experiments carried out on grafts of Arabidopsis thaliana intended for differential expression analyses. |
nbinomDensity |
Lists all currently available densityFunctions. |
normDensity |
Lists all currently available densityFunctions. |
pairData |
Simulated data for testing the baySeq package methods for paired data |
pairedData |
baySeq - classes |
pairedData-class |
baySeq - classes |
plotMA.CD |
'MA'-plot for count data. |
plotNullPrior |
Plots distribution of null function and shows the threshold separator. |
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 |
replicates |
baySeq - classes |
replicates-method |
baySeq - classes |
replicates<- |
baySeq - classes |
replicates<--method |
baySeq - classes |
seglens |
baySeq - classes |
seglens-method |
baySeq - classes |
seglens<- |
baySeq - classes |
seglens<--method |
baySeq - classes |
selectTop |
Selects the top genomic events, based on posterior likelihoods, from a 'countData' object. |
show-method |
baySeq - classes |
simData |
Simulated data for testing the baySeq package methods |
summarisePosteriors |
Summarises expected number of genomic events given the calculated posterior likelihoods of a countData object. |
topCounts |
Get the top counts corresponding to some group from a 'countData' object |
zimData |
Simulated data for testing the baySeq package methods |
ZINBDensity |
Lists all currently available densityFunctions. |
[-method |
baySeq - classes |