man/genotypeInf.Rd
 f0f8ba16  \name{genotypeInf} \alias{genotypeInf} \title{ Genotyping of Illumina Infinium II arrays. } \description{ Genotyping of Illumina Infinium II arrays. This function  808cfecc  provides CRLMM/KRLMM genotypes and confidence scores for the the  f0f8ba16  polymorphic markers and is a required step prior to copy number estimation. } \usage{  7c0c9ac5  genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams =  ba1a7d73  TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm", trueCalls = NULL)  f0f8ba16  } %- maybe also 'usage' for other objects documented here. \arguments{ \item{cnSet}{An object of class \code{CNSet}} \item{mixtureParams}{ \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 batchQC)} \item{gender}{ integer vector ( male = 1, female =2 ) or missing, with same length as filenames. If missing, the gender is predicted.}  7c0c9ac5  \item{DF}{'integer' with number of degrees of freedom to use with t-distribution.} \item{cdfName}{\code{character} string indicating which annotation package to load.}  808cfecc  \item{call.method}{character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').}  ba1a7d73  \item{trueCalls}{ matrix specifying known Genotype calls for a subset of samples and features(1 - AA, 2 - AB, 3 - BB).}  f0f8ba16  } \details{  808cfecc  The genotype calls and confidence scores are written to  f0f8ba16  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.  ba1a7d73  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).  f0f8ba16  } \value{ 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. } \author{ R. Scharpf } \seealso{  7c0c9ac5  \code{\link{crlmm}}, \code{\link{snpCall}}, \code{\link{snpCallProbability}}, \code{\link{annotationPackages}}  f0f8ba16  } \examples{ ## See the 'illumina_copynumber' vignette in inst/scripts of ## the source package } \keyword{classif}