\name{copynumberAccessors}
 \alias{CA}
 \alias{CB}

 \alias{nuA}
 \alias{nuB}
 \alias{phiA}
 \alias{phiB}

 \alias{totalCopynumber}

 \alias{rawCopynumber}

 
 \title{
 
 	Accessors for allele-specific or total copy number
 
 }
 
 
 \description{
 
 These methods can be applied after an object of class \code{CNSet} has
 been generated by the \code{crlmmCopynumber} function.
 
 }
 \usage{
 CA(object, ...)
 CB(object, ...)

 nuA(object)
 nuB(object)
 phiA(object)
 phiB(object)

 totalCopynumber(object,...)

 rawCopynumber(object,...)

 }
 
 \arguments{

   \item{object}{  An object of class \code{CNSet}.}

   \item{\dots}{
   An additional argument named 'i' can be passed to subset the markers
   and an argument 'j' can be passed to subset the samples.  Other
   arguments are ignored.

   }

 }
 
 \details{
 

 	At polymorphic markers, nuA and nuB provide the intercept
 	coefficient (the estimated background intensity) for the A and
 	B alleles, respectively. phiA and phiB provide the slope
 	coefficients for the A and B alleles, respectively.
 
 	At nonpolymorphic markers, nuB and phiB are 'NA'.
 

 	These functions can be used to tranlate the normalized
 	intensities to the copy number scale.  Plotting the copy
 	number estimates as a function of physical position can be
 	used to guide downstream algorithms that smooth, as well as to
 	assess possible mosaicism.
 

 }

 \value{

 
 	nu[A/B] and phi[A/B] return matrices of the intercept and

 	slope coefficients, respectively.

 	CA and CB return matrices of allele-specific copy number.

 	totalCopynumber (or rawCopynumber) returns a matrix of CA+CB.

       }
 
 \note{
 
 Subsetting the \code{CNSet} object before extracting copy number can be
 very inefficient when the data set is very large, particularly if using

 ff objects.  The \code{[} method will subset all of the assay data

 elements and all of the elements in the LinearModelParameter slot.
 

 }
 

 \seealso{

 
 	\code{\link{crlmmCopynumber}}, \code{\link{CNSet-class}}
 

 }

 \examples{

 \dontrun{

 data(cnSetExample)
 all(isCurrent(cnSetExample)) ## is the cnSet object current?

 
 ## --------------------------------------------------
 ## calculating allele-specific copy number
 ## --------------------------------------------------
 ## copy number for allele A, first 5 markers, first 2 samples

 (ca <- CA(cnSetExample, i=1:5, j=1:2))

 ## copy number for allele B, first 5 markers, first 2 samples

 (cb <- CB(cnSetExample, i=1:5, j=1:2))

 ## total copy number for first 5 markers, first 2 samples
 (cn1 <- ca+cb)
 
 ## total copy number at first 5 nonpolymorphic loci

 index <- which(!isSnp(cnSetExample))[1:5]
 cn2 <- CA(cnSetExample, i=index, j=1:2)

 ## note, cb is NA at nonpolymorphic loci

 (cb <- CB(cnSetExample, i=index, j=1:2))

 ## note, ca+cb will give NAs at nonpolymorphic loci

 CA(cnSetExample, i=index, j=1:2) + cb

 ## A shortcut for total copy number

 cn3 <- totalCopynumber(cnSetExample, i=1:5, j=1:2)

 all.equal(cn3, cn1)

 cn4 <- totalCopynumber(cnSetExample, i=index, j=1:2)

 all.equal(cn4, cn2)
 
 ## markers 1-5, all samples

 cn5 <- totalCopynumber(cnSetExample, i=1:5)

 ## all markers, samples 1-5

 cn6 <- totalCopynumber(cnSetExample, j=1:2)

 }

 }
 \keyword{manip}