| 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}
|
