baySeq - classes
Data from a set of small RNA sequencing experiments carried out
on grafts of Arabidopsis thaliana intended for differential expression
analyses.
Summarises expected number of genomic events given the calculated
posterior likelihoods of a countData object.
Simulated data for testing the baySeq package methods for paired data
Finds posterior likelihoods for each count or paired count as
belonging to some model.
Estimates prior parameters for the underlying distributions of
'count' data.
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.
Lists all currently available densityFunctions.
'MA'-plot for count data.
`countData' object derived from data file `simData' with
estimated priors.
Gets the number of true positives in the top n counts selected by
ranked posterior likelihoods
Construct orderings for count data given a model structure and an
ordering function.
Selects the top genomic events, based on posterior likelihoods, from a
`countData' object.
An internal function in the baySeq package for calculating
posterior likelihoods given likelihoods of the data.
Empirical Bayesian analysis of patterns of differential expression in count data.
Function to generate all possible models for a countData object based
on the replicate data.
Plots the posterior likelihoods estimated for a 'countData' object
against the log-ratios observed between two sets of sample data.
Plots distribution of null function and shows the threshold separator.
Get the top counts corresponding to some group from a
'countData' object
Class "densityFunction"
Annotation data for a set of small RNA loci derived from sequencing
of grafts of Arabidopsis thaliana intended for differential expression
analyses.
Generation of intermediate values in likelihood estimation for methylation
data.
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
Simulated data for testing the baySeq package methods
Estimates library scaling factors (library sizes) for count data.
`countData' object derived from data file `simData' with
estimated likelihoods of differential expression.
Simulated data for testing the baySeq package methods