\name{calculateRBaf}
 \alias{calculateRBaf}
 \alias{calculateRBaf,CNSet-method}
 \title{Calculate log R ratios and B allele frequencies.}
 \description{Calculate log R ratios and B allele frequencies from
   a \code{CNSet} object}
 \usage{
 calculateRBaf(object, batch.name)
 }
 
 \arguments{
   \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.
 
 }
 
 \value{
   A list.
 
   \code{baf}: A matrix of B allele frequencies.
 
   \code{lrr}: A matrix of log R ratios.
 
 }
 
 \references{
 
   Reference for BAFs, LRRs.
 
 }
 \author{Lynn Mireless}
 
 \examples{

 data(cnSetExample)
 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.
 \keyword{list}
 \keyword{methods}