baySeq (version 2.6.0)

allModels: 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.

Value

A countData with populated `@groups' 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.

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)