allModels {baySeq} | R Documentation |
This function populates the ‘@groups’ slot of the supplied countData object with all possible models for equivalence/non-equivalence of expression between replicate groups.
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)
# 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)