man/preprocessInf.Rd
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 \name{preprocessInf}
 \alias{preprocessInf}
 \title{
 
 	Preprocessing of Illumina Infinium II arrays.
 
 }
 \description{
 
 	This function normalizes the intensities for the 'A' and 'B'
 	alleles for a \code{CNSet} object and estimates mixture
 	parameters used for subsequent genotyping.  See details for
 	how the normalized intensities are written to file.  This step
 	is required for subsequent genotyping and copy number
 	estimation.
 
 }
 \usage{
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 preprocessInf(cnSet, sampleSheet=NULL, arrayNames = NULL, ids = NULL,
 path = ".", arrayInfoColNames = list(barcode = "SentrixBarcode_A",
 position = "SentrixPosition_A"), highDensity = TRUE, sep = "_", fileExt
 = list(green = "Grn.idat", red = "Red.idat"), saveDate = TRUE, stripNorm
 = TRUE, useTarget = TRUE, mixtureSampleSize = 10^5, fitMixture = TRUE,
 eps = 0.1, verbose = TRUE, seed = 1, cdfName)
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 }
 
 \arguments{
   \item{cnSet}{
   object of class \code{CNSet}
 }
 
   \item{sampleSheet}{\code{data.frame} containing Illumina sample sheet
     information (for required columns, refer to BeadStudio Genotyping
     guide - Appendix A).}
 
   \item{arrayNames}{character vector containing names of arrays to be
     read in.  If \code{NULL}, all arrays that can be found in the
     specified working directory will be read in.}
 
   \item{ids}{vector containing ids of probes to be read in.  If
     \code{NULL} all probes found on the first array are read in.}
 
   \item{path}{character string specifying the location of files to be
     read by the function}
 
   \item{arrayInfoColNames}{(used when \code{sampleSheet} is specified)
     list containing elements 'barcode' which indicates column names in
     the \code{sampleSheet} which contains the arrayNumber/barcode number
     and 'position' which indicates the strip number.  In older style
     sample sheets, this information is combined (usually in a column
     named 'SentrixPosition') and this should be specified as
     \code{list(barcode=NULL, position="SentrixPosition")}}
 
   \item{highDensity}{logical (used when \code{sampleSheet} is
     specified). If \code{TRUE}, array extensions '\_A', '\_B' in
     sampleSheet are replaced with 'R01C01', 'R01C02' etc.}
   \item{sep}{character string specifying separator used in .idat file
     names.}
   \item{fileExt}{list containing elements 'Green' and 'Red' which
     specify the .idat file extension for the Cy3 and Cy5 channels.}
   \item{saveDate}{'logical'.  Should the dates from each .idat be saved
     with sample information?}
   \item{stripNorm}{'logical'.  Should the data be strip-level normalized?}
   \item{useTarget}{'logical' (only used when \code{stripNorm=TRUE}).
     Should the reference HapMap intensities be used in strip-level normalization?}
   \item{mixtureSampleSize}{ Sample size to be use when fitting the mixture model.}
   \item{fitMixture}{ 'logical.' Whether to fit per-array mixture
     model. }
   \item{eps}{   Stop criteria.}
   \item{verbose}{  'logical.'  Whether to print descriptive messages during processing.}
   \item{seed}{ Seed to be used when sampling. Useful for
     reproducibility}
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   \item{cdfName}{ \code{character} string indicating which annotation
     package to load.}
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 }
 \details{
 
 	The normalized intensities are written to disk using package
 	\code{ff} protocols for writing/reading to disk. Note that the
 	object \code{CNSet} containing the \code{ff} objects in the
 	\code{assayData} slot will be updated after applying this
 	function.
 
 }
 \value{
 
 	A \code{ff_matrix} object containing parameters for fitting the
 	mixture model.  Note that while the \code{CNSet} object is not
 	returned by this function, the object will be updated as the
 	normalized intensities are written to disk.  In particular,
 	after applying this function the normalized intensities in the
 	\code{alleleA} and \code{alleleB} elements of \code{assayData}
 	are now available.
 
 }
 \author{
 R. Scharpf
 }
 \seealso{
 	\code{\link{CNSet-class}}, \code{\link{A}}, \code{\link{B}},
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 	\code{\link{constructInf}}, \code{\link{genotypeInf}}, \code{\link{annotationPackages}}
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 }
 \examples{
 	## See the 'illumina_copynumber' vignette in inst/scripts of
 	## the source package
 }
 \keyword{manip}