Objects from the Class
Objects can be created by calls of the form new("ExomeDepth",
data = NULL, test, reference, formula = 'cbind(test, reference) ~
1', subset.for.speed = NULL).
data is optional and is only used if the formula
argument refers to covariates (in which case these covariates must be
included in the data frame).
test and reference refer to the read count data for the
test and reference samples.
Creating a ExomeDepth object will automatically fit the beta-binomial
model (using routines from the aod package) and compute the
likelihood for the three copy number states (normal, deletion and
duplication).