This object is a list containing the basic data elements required for the HMM
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).
A HapMap sample on the Affymetrix 50k platform. Chromosomal alterations were simulated. The last 100 SNPs on chromosome 2 are, in fact, a repeat of the first 100 SNPs on chromosome 1 – this was added for internal use.
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