\name{genotypeAffy}
 \alias{genotypeAffy}
 \title{Genotype Affymetrix CEL files}
 \description{Assign diallelic genotypes at polymorphic markers}
 \usage{
 genotypeAffy(cnSet, SNRMin = 5, recallMin = 10, recallRegMin = 1000, gender = NULL, badSNP = 0.7, returnParams = TRUE, verbose = TRUE)
 }
 
 \arguments{
   \item{cnSet}{
     An object of class \code{CNSet}
   }
   \item{SNRMin}{
     See \code{\link{crlmm}}
   }
   \item{recallMin}{
     See \code{\link{crlmm}}
 }
   \item{recallRegMin}{
     See \code{\link{crlmm}}
 }
   \item{gender}{
     See \code{\link{crlmm}}
 }
   \item{badSNP}{
     See \code{\link{crlmm}}
 }
   \item{returnParams}{
     See \code{\link{crlmm}}
 }
   \item{verbose}{
     Logical.
 }
 }
 \details{
   Wrapper for crlmm genotyping.
 }
 \value{
   Returns logical.  SNP genotypes and confidence scores are written to
   \code{ff_matrix} objects.
 }
 
 \author{
 R.Scharpf
 }
 \seealso{
   \code{\link{crlmm}}, \code{\link{calls}}, \code{\link{confs}}
 }
 \keyword{classif}