baySeq: Empirical Bayesian analysis of patterns of differential expression in count data
Version 2.10.0

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

Browse man pages Browse package API and functions Browse package files

AuthorThomas J. Hardcastle
Bioconductor views DifferentialExpression MultipleComparison SAGE Sequencing
Date of publicationNone
MaintainerThomas J. Hardcastle <tjh48@cam.ac.uk>
LicenseGPL-3
Version2.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("baySeq")

Man pages

allModels: Function to generate all possible models for a countData...
baySeq-classes: baySeq - classes
baySeq-package: Empirical Bayesian analysis of patterns of differential...
bimodalSep: A function that, given a numeric vector, finds the value...
CDPost: 'countData' object derived from data file 'simData' with...
CDPriors: 'countData' object derived from data file 'simData' with...
densityFunction: Class '"densityFunction"'
densityFunctions: Lists all currently available densityFunctions.
getLibsizes: Estimates library scaling factors (library sizes) for count...
getLikelihoods: Finds posterior likelihoods for each count or paired count as...
getPosteriors: An internal function in the baySeq package for calculating...
getPriors: Estimates prior parameters for the underlying distributions...
getTPs: Gets the number of true positives in the top n counts...
makeOrderings: Construct orderings for count data given a model structure...
marginaliseEqual: Computes marginal likelihoods that two replicate groups are...
marginalisePairwise: Computes marginal likelihoods that two replicate groups...
methObservables: Generation of intermediate values in likelihood estimation...
mobAnnotation: Annotation data for a set of small RNA loci derived from...
mobData: Data from a set of small RNA sequencing experiments carried...
pairData: Simulated data for testing the baySeq package methods for...
plotMA.CD: 'MA'-plot for count data.
plotNullPrior: Plots distribution of null function and shows the threshold...
plotPosteriors: Plots the posterior likelihoods estimated for a 'countData'...
plotPriors: Plots the density of the log values estimated for the mean...
selectTop: Selects the top genomic events, based on posterior...
simData: Simulated data for testing the baySeq package methods
summarisePosteriors: Summarises expected number of genomic events given the...
topCounts: Get the top counts corresponding to some group from a...
zimData: Simulated data for testing the baySeq package methods

Functions

CDPost Man page
CDPriors Man page
ZINBDensity Man page
[,countData,ANY-method Man page
[,countData-method Man page
[,pairedData-method Man page
allModels Man page Source code
baySeq Man page
baySeq-class Man page
baySeq-classes Man page
baySeq-package Man page
bbDensity Man page
bbNCDist Man page
betaBinomialFunction Source code
betaBinomialNCFunction Source code
bimodalKernel Source code
bimodalSep Source code
bimodalSeparator Man page Source code
catObservables Source code
ciEstimator Source code
constructWeights Source code
controlFDR Source code
controlFWER Source code
countData Man page
countData-class Man page
dZINB Source code
densityFunction Man page
densityFunction,countData-method Man page
densityFunction-class Man page
densityFunction<- Man page
densityFunction<-,countData-method Man page
densityFunctions Man page Source code
dim,countData-method Man page
fastUniques Source code
getLibsizes Man page
getLikelihoods Man page
getLikelihoods.BB Man page
getLikelihoods.NB Man page
getPosteriors Man page
getPriors Man page
getPriors.NB Man page
getTPs Man page Source code
groups Man page
groups,countData-method Man page
groups<- Man page
groups<-,countData-method Man page
libsizes Man page
libsizes,countData-method Man page
libsizes,pairedData-method Man page
libsizes<- Man page
libsizes<-,countData-method Man page
libsizes<-,pairedData-method Man page
logRowSum Source code
logsum Source code
makeOrderings Man page Source code
marginaliseEqual Man page Source code
marginalisePairwise Man page Source code
md2Density Man page
md3Density Man page
mdDensity Man page
methObservables Man page Source code
mobAnnotation Man page
mobData Man page
multiDirichletFunction Source code
multiDirichletFunction2 Source code
multiDirichletFunction3 Source code
multiSymDirichletFunction Source code
nbinomDens Source code
nbinomDensity Man page
normDensity Man page
normDensityFunction Source code
oldmethObservables Source code
pairData Man page
pairedData Man page
pairedData-class Man page
pasteMatrixColon Source code
plotMA.CD Man page Source code
plotNullPrior Man page Source code
plotPosteriors Man page Source code
plotPriors Man page
posteriorWeights Source code
rbind Man page
rbind,countData-method Man page
replicates Man page
replicates,countData-method Man page
replicates<- Man page
replicates<-,countData-method Man page
seglens Man page
seglens,countData-method Man page
seglens<- Man page
seglens<-,countData-method Man page
selectPosteriors Source code
selectTags Source code
selectTop Man page Source code
show,countData-method Man page
show,pairedData-method Man page
showData Source code
simData Man page
sliceArray Source code
summarisePosteriors Man page Source code
topCounts Man page
zimData Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/allModels.R
R/betaBinomial.R
R/bimodalSep.R
R/bimodalSeparator.R
R/countData-accessors.R
R/densDensityFunctions.R
R/densityFunction-accessors.R
R/densityFunctions.R
R/getLibsizes.R
R/getLikelihoods.NB.R
R/getLikelihoods.R
R/getPriors.LN.R
R/getPriors.R
R/getPriors_Generic.R
R/getTPs.R
R/marginalisePairwise.R
R/plotMA.CD.R
R/plotPosteriors.R
R/plotPriors.R
R/summarisePosteriors.R
R/topCounts.R
R/utilityFunctions.R
build
build/vignette.rds
data
data/CDPost.RData
data/CDPriors.RData
data/mobAnnotation.RData
data/mobData.RData
data/pairData.RData
data/simData.RData
data/zimData.RData
inst
inst/doc
inst/doc/baySeq.R
inst/doc/baySeq.Rnw
inst/doc/baySeq.pdf
inst/doc/baySeq_generic.R
inst/doc/baySeq_generic.Rnw
inst/doc/baySeq_generic.pdf
man
man/CDPost.Rd
man/CDPriors.Rd
man/allModels.Rd
man/baySeq-classes.Rd
man/baySeq-package.Rd
man/bimodalSep.Rd
man/densityFunction.Rd
man/densityFunctions.Rd
man/getLibsizes.Rd
man/getLikelihoods.Rd
man/getPosteriors.Rd
man/getPriors.Rd
man/getTPs.Rd
man/makeOrderings.Rd
man/marginaliseEqual.Rd
man/marginalisePairwise.Rd
man/methObservables.Rd
man/mobAnnotation.Rd
man/mobData.Rd
man/pairData.Rd
man/plotMA.CD.Rd
man/plotNullPrior.Rd
man/plotPosteriors.Rd
man/plotPriors.Rd
man/selectTop.Rd
man/simData.Rd
man/summarisePosteriors.Rd
man/topCounts.Rd
man/zimData.Rd
vignettes
vignettes/baySeq.Rnw
vignettes/baySeq_generic.Rnw
vignettes/priorlog.txt
baySeq documentation built on May 20, 2017, 10:27 p.m.