Browse code

Export low-level processing function readIDAT() (as requested by Kasper Daniel Hansen)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@56864 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 21/07/2011 04:29:31
Showing3 changed files

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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.11.2
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+Version: 1.11.3
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -66,6 +66,7 @@ export(crlmm,
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        crlmmIllumina,
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        crlmmIlluminaV2,
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        genotype,
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+       readIDAT,
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        readIdatFiles,
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        snprma,
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        snprma2,
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new file mode 100644
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+\name{readIDAT}
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+\alias{readIDAT}
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+\alias{readIDAT}
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+
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+\title{Low-level function to read idat files}
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+
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+\description{
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+  Reads intensity information for each bead type from a single .idat file 
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+  from Infinium II platforms.  This is a low-level function which \code{readIdatFiles} 
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+  is a wrapper to}
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+
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+\usage{
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+readIDAT(idatFile)
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+}
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+
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+\arguments{
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+  \item{idatFile}{character string specifying idat file to be read in}
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+}
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+
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+\details{
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+This fuction returns a list containing summarised intensities and other 
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+information extracted from a single .idat file.
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+
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+The \code{readIdatFiles} function makes use of \code{readIDAT} to read 
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+the paired Cy3 and Cy5 idats from one or more arrays.
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+
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+Thanks to Keith Baggerly who providing this code.
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+}
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+
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+\value{
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+  list which includes item \code{Quants} which contains average intensity (\code{Mean}),
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+  number of beads (\code{NBeads}) and measure of variability (\code{SD}) for 
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+  each bead type on the array.
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+}
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+
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+\references{
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+  Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
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+  R/Bioconductor software for Illumina's Infinium whole-genome 
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+  genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.
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+}
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+
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+\author{Keith Baggerly, with modifications from Matt Ritchie}
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+
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+\examples{
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+
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+#idatlist = readIDAT("4019585367_A_Grn.idat")
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+
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+}
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+\keyword{IO}