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baySeq (version 2.6.0)

Empirical Bayesian analysis of patterns of differential expression in count data

Description

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.

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Version

Version

2.6.0

License

GPL-3

Maintainer

Thomas J Hardcastle

Last Published

February 15th, 2017

Functions in baySeq (2.6.0)

baySeq-classes

baySeq - classes
mobData

Data from a set of small RNA sequencing experiments carried out on grafts of Arabidopsis thaliana intended for differential expression analyses.
summarisePosteriors

Summarises expected number of genomic events given the calculated posterior likelihoods of a countData object.
pairData

Simulated data for testing the baySeq package methods for paired data
getLikelihoods

Finds posterior likelihoods for each count or paired count as belonging to some model.
getPriors

Estimates prior parameters for the underlying distributions of 'count' data.
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.
densityFunctions

Lists all currently available densityFunctions.
plotMA.CD

'MA'-plot for count data.
CDPriors

`countData' object derived from data file `simData' with estimated priors.
getTPs

Gets the number of true positives in the top n counts selected by ranked posterior likelihoods
makeOrderings

Construct orderings for count data given a model structure and an ordering function.
selectTop

Selects the top genomic events, based on posterior likelihoods, from a `countData' object.
getPosteriors

An internal function in the baySeq package for calculating posterior likelihoods given likelihoods of the data.
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.
plotPosteriors

Plots the posterior likelihoods estimated for a 'countData' object against the log-ratios observed between two sets of sample data.
plotNullPrior

Plots distribution of null function and shows the threshold separator.
topCounts

Get the top counts corresponding to some group from a 'countData' object
densityFunction-class

Class "densityFunction"
mobAnnotation

Annotation data for a set of small RNA loci derived from sequencing of grafts of Arabidopsis thaliana intended for differential expression analyses.
methObservables

Generation of intermediate values in likelihood estimation for methylation 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
simData

Simulated data for testing the baySeq package methods
getLibsizes

Estimates library scaling factors (library sizes) for count data.
CDPost

`countData' object derived from data file `simData' with estimated likelihoods of differential expression.
zimData

Simulated data for testing the baySeq package methods