\HeaderA{locusLevelData}{Basic data elements required for the HMM}{locusLevelData}
\keyword{datasets}{locusLevelData}
\begin{Description}\relax
This object is a list containing the basic data elements required for the HMM
\end{Description}
\begin{Usage}
\begin{verbatim}data(locusLevelData)\end{verbatim}
\end{Usage}
\begin{Format}\relax
A list
\end{Format}
\begin{Details}\relax
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).
\end{Details}
\begin{Source}\relax
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.
\end{Source}
\begin{Examples}
\begin{ExampleCode}
data(locusLevelData)
str(locusLevelData)
\end{ExampleCode}
\end{Examples}

