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.
Critically, it is not required to store the positions of the DNA fragments
that led to the test and reference counts. That is only required for the
function TestCNV. If this is of use, a GRanges object can be provided
using the argument positions.
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).