Genotyping of Illumina Infinium II arrays.
 	Genotyping of Illumina Infinium II arrays. This function
 	provides CRLMM/KRLMM genotypes and confidence scores for the the
 	polymorphic markers and is a required step prior to copy
 	number estimation.
 genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5,
 recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams =
 TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm", 
 trueCalls = NULL)
 %- maybe also 'usage' for other objects documented here.
   \item{cnSet}{An object of class \code{CNSet}}
     \code{data.frame} containing mixture model parameters needed for
     genotyping.  The mixture model parameters are estimated from the
     \code{preprocessInf} function.
   \item{probs}{'numeric' vector with priors for AA, AB and BB.}
   \item{SNRMin}{'numeric' scalar defining the minimum SNR used to filter
     out samples.}
   \item{recallMin}{Minimum number of samples for recalibration. }
   \item{recallRegMin}{Minimum number of SNP's for regression.}
   \item{verbose}{  'logical.'  Whether to print descriptive messages during processing.}
   \item{returnParams}{'logical'. Return recalibrated parameters from crlmm.}
   \item{badSNP}{'numeric'. Threshold to flag as bad SNP (affects
   \item{gender}{  integer vector (  male = 1, female =2 ) or missing,
   with same length as filenames.  If missing, the gender is
   \item{DF}{'integer' with number of degrees of freedom to use with
   \item{cdfName}{\code{character} string indicating which annotation
     package to load.}
   \item{call.method}{character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').}
   \item{trueCalls}{ matrix specifying known Genotype calls for a subset of samples and features(1 - AA, 2 - AB, 3 - BB).}
 	The genotype calls and confidence scores are written to
 	file using \code{ff} protocols for I/O.  For the most part,
 	the calls and confidence scores can be accessed as though the
 	data is in memory through the methods \code{snpCall} and
 	\code{snpCallProbability}, respectively.
 	The genotype calls are stored using an integer representation: 1
 	- AA, 2 - AB, 3 - BB.  Similarly, the call probabilities are
 	stored using an integer representation to reduce file size using
 	the transformation 'round(-1000*log2(1-p))', where p is the
 	probability.  The function \code{i2P} can be used to convert the
 	integers back to the scale of probabilities.
 	An optional \code{trueCalls} argument can be provided to KRLMM method
 	which contains known genotype calls(can contain some NAs) for some 
 	samples and SNPs. This will used to compute KRLMM parameters by calling
 	\code{vglm} function from \code{VGAM} package.
 	The KRLMM method makes use of functions provided in \code{parallel} 
 	package to speed up the process. It by default initialises up to 
 	8 clusters. This is configurable by setting up an option named 
 	"krlmm.cores", e.g. options("krlmm.cores" = 16). 
 Logical.  If the genotyping is completed, the value 'TRUE' is
 returned.  Note that \code{assayData} elements 'call' and
 'callProbability' are updated on disk. Therefore, the genotypes and
 confidence scores can be retrieved using accessors for the
 \code{CNSet}  class.
 R. Scharpf
 	\code{\link{crlmm}}, \code{\link{snpCall}},
 	\code{\link{snpCallProbability}}, \code{\link{annotationPackages}}
 	## See the 'illumina_copynumber' vignette in inst/scripts of
 	## the source package