Accessors for allele-specific or total copy number



These methods can be applied after an object of class \code{CNSet} has
been generated by the \code{crlmmCopynumber} function.

CA(object, ...)
CB(object, ...)

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


	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.



	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.



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.



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


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)