allModels {baySeq} | R Documentation

## Function to generate all possible models for a countData object based on the replicate data.

### Description

This function populates the ‘@groups’ slot of the supplied countData object with all possible models for equivalence/non-equivalence of expression between replicate groups.

### Usage

    allModels(CD)

### Arguments

`CD` | A countData object with a populated ‘@replicates’ slot.

### Details

Given a large number of different replicate groups, the total number of possible models listed in the ‘@groups’ slot rises exponentially. This function will attempt to list them all. The use of consensus priors (see `getPriors`) is recommended if the number of models is high.

### Value

A `countData` with populated ‘@groups’ slot.

### Author(s)

Thomas J. Hardcastle

### References

Hardcastle T.J., and Kelly, K. baySeq: Empirical Bayesian Methods For Identifying Differential Expression In Sequence Count Data. BMC Bioinformatics (2010)

### See Also

`getPriors`

### Examples

    # load test data
    data(simData)

    # Create a {countData} object from test data, supposing that there are
    # multiple experimental groups present.

    replicates <- c("simA", "simA", "simB", "simC", "simC", "simD", "simE", "simE", "simF", "simG")
    CD <- new("countData", data = simData, replicates = replicates)
    CD <- allModels(CD)

    # The total number of models generated is high.
    length(CD@groups)

[Package baySeq version 2.28.0 Index]