\name{readIdatFiles}
\alias{readIdatFiles}

\title{Reads Idat Files from Infinium II Illumina BeadChips}

\description{
  Reads intensity information for each bead type from
  .idat files of Infinium II genotyping BeadChips}

\usage{
readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",
              arrayInfoColNames=list(barcode="SentrixBarcode_A",
                                     position="SentrixPosition_A"),
              highDensity=FALSE, sep="_",
              fileExt=list(green="Grn.idat", red="Red.idat"),
              saveDate=FALSE)
}

\arguments{
  \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?}
}

\details{
The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that
were used in each channel and standard errors (all on the orginal scale)
are read in from the .idat files.

Where available, a \code{sampleSheet} data.frame, in the same format
as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and
'SentrixPosition\_A' are required) which keeps track of sample
information can be specified.

Thanks to Keith Baggerly who provided the code to read in the binary .idat files.
}

\value{
  NChannelSet with intensity data (\code{R}, \code{G}), number of beads
  (\code{Rnb}, \code{Gnb}) and standard errors (\code{Rse}, \code{Gse})
  for each bead type.
}

\author{Matt Ritchie}

\examples{

#RG = readIdatFiles()

}
\keyword{IO}