\title{Calculate log R ratios and B allele frequencies.}
\description{Calculate log R ratios and B allele frequencies from
  a \code{CNSet} object}
calculateRBaf(object, batch.name)

  \item{object}{A \code{CNSet} object.}
  \item{batch.name}{A character string.  See details.}
\details{\code{batch.name} must be a value in
  \code{batch(object)}. Currently, one must specify a single
  \code{batch.name}. If a character vector for \code{batch.name} is
  supplied, only the first is evaluated.

  TODO: A description of how these values are calculated.


  A list.

  \code{baf}: A matrix of B allele frequencies.

  \code{lrr}: A matrix of log R ratios.



  Reference for BAFs, LRRs.

\author{Lynn Mireless}

baf.lrr <- calculateRBaf(cnSetExample, "SHELF")
hist(baf.lrr[["baf"]], breaks=100)
hist(baf.lrr[["lrr"]], breaks=100)
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.