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Added man page for readGenCallOutput()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59152 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 13/10/2011 05:40:07
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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: 1.11.60
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+Version: 1.11.61
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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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@@ -60,6 +60,7 @@ export(crlmm,
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        genotype,
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        readIDAT,
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        readIdatFiles,
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+       readGenCallOutput,
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        snprma,
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        snprma2,
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        crlmm2,
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new file mode 100644
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+\name{readGenCallOutput}
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+\alias{readGenCallOutput}
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+
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+\title{Read X and Y intensities from GenCall output}
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+
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+\description{
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+  This function reads the raw X and Y intensities output by GenomeStudio's GenCall genotyping module in preparation for genotyping with \code{crlmm}.
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+}
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+
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+\usage{
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+readGenCallOutput(file, path=".", cdfName, colnames=list("SampleID"="Sample ID", "SNPID"="SNP Name", "XRaw"="X Raw", "YRaw"="Y Raw"),
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+                  type=list("SampleID"="character", "SNPID"="character", "XRaw"="integer", "YRaw"="integer"), verbose=FALSE)
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+}
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+
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+\arguments{
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+  \item{file}{'character' string specifying the name of the file to read in}
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+  \item{path}{'character' string specifying the location of file to be read by the function}
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+  \item{cdfName}{'character' defining the chip annotation (manifest) to use
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+    ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',
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+    'human370quadv3c', 'human610quadv1b', 'human660quadv1a',
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+    'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')}
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+  \item{cdfName}{'character' defining the chip annotation (manifest) to use
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+  \item{colnames}{list containing elements 'SampleID', 'SNPID', 'XRaw' and 'YRaw', which specify the column names from
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+     in 'file' that pertain to these variables.  The default should suffice in most situations. 
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+  \item{type}{list containing data types for the columns to be read in.  The default should be fine in most situations.
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+  \item{verbose}{'logical'.  Should processing information be displayed as data is read in?}
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+}
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+
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+\details{
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+This function returns an \code{NChannelSet} containing raw intensity data (X and Y) from GenCall final report file. 
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+It assumes that the data is in the format where the GenCall results are listed sample by sample below the one and other,
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+an that the columns 'X Raw' and 'Y Raw' are available in the file.
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+The function crlmmillumina() can be run on the output of the \code{readGenCallOutyputis function. 
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+}
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+
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+\value{
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+\code{NChannelSet} containing X and Y bead intensities.
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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{Cynthia Liu and Matt Ritchie}
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+
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+\examples{
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+
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+#XY = readGenCallOutput(file="Hap650Yv3_Final_Report.txt", cdfName="human650v3a")
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+#crlmmOut = crlmmIllumina(XY=XY)
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+
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+}
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+
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+\keyword{IO}