The basic assay data elements that can be used for fitting the HMM
are: 1. a mapping of platform identifiers to chromosome and physical
position
2. (optional) a matrix of copy number estimates
3. (optional) a matrix of confidence scores for the copy number
estimates (e.g., inverse standard deviations)
4. (optional) a matrix of genotype calls
5. (optional) CRLMM confidence scores for the genotype calls
At least (2) or (4) is required. The locusLevelData is a list that
contains (1), (2), (4), and (5).