allModels: Function to generate all possible models for a countData...
In baySeq: Empirical Bayesian analysis of patterns of differential expression in count data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	allModels(CD)

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

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.

A countData with populated ‘@groups’ slot.

Thomas J. Hardcastle

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

getPriors

# 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)