\name{SnpSet-methods}
\docType{methods}
\alias{calls}
\alias{calls,SnpSet-method}
\alias{calls<-}
\alias{calls<-,SnpSet,matrix-method}
\alias{confs}
\alias{confs,SnpSet-method}
\alias{confs<-}
\alias{confs<-,SnpSet,matrix-method}
\title{Accessors for Calls and Confidences on a SnpSet object}
\description{
  \code{calls} returns the genotype calls. CRLMM stores genotype calls
  as integers (1 - AA; 2 - AB; 3 - BB).

  \code{confs} returns the confidences associated to the genotype
  calls. The current implementation of CRLMM stores the confidences as
  integers by using the transformation:

  conf = round(-1000*log2(1-p)),

  where 'p' is the posterior probability of the call.
}

\section{Methods}{
	\describe{
	\item{\code{initialize(SnpSet)}:}{Object instantiation, used by
	  \code{new}; not to be called directly by the user.}  
	\item{\code{calls(object)}:}{accessor for genotype calls}
	\item{\code{confs(object)}:}{accessor for crlmm genotype confidence scores}
	}
}
\seealso{\code{\link{addFeatureAnnotation}}}
\examples{

	theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
	p <- matrix(runif(20), nc=2)
	theConfs <- round(-1000*log2(1-p))
	obj <- new("SnpSet", call=theCalls, callProbability=theConfs)
	calls(obj)
	confs(obj)

##	if(require("genomewidesnp6Crlmm")){
##		ids <- c("SNP_A-2131660", "SNP_A-1967418", "SNP_A-1969580", "SNP_A-4263484",
##			 "SNP_A-1978185", "SNP_A-4264431", "SNP_A-1980898", "SNP_A-1983139",
##			 "SNP_A-4265735", "SNP_A-1995832")
##		rownames(theCalls) <- rownames(p) <- rownames(theConfs) <- ids
##		obj <- new("SnpSet", call=theCalls, callProbability=theConfs,
##			   annotation="genomewidesnp6")
##		obj2 <- annotate(obj)
##		fvarLabels(obj2)
##	}
}
\keyword{manip}