@@ -23,6 +23,10 @@ been generated by the \code{crlmmCopynumber} function.

 \usage{

 CA(object, ...)

 CB(object, ...)

+nuA(object)

+nuB(object)

+phiA(object)

+phiB(object)

 totalCopynumber(object,...)

 }

@@ -37,15 +41,31 @@ totalCopynumber(object,...)

 \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{

-	A matrix of allele-specific or total copy number estimates.

+

+	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 returns a matrix of CA+CB.

+

 }

 \seealso{