1. crlmm
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Add doc for cnSetExample

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59041 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/10/2011 12:18:21
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DESCRIPTION
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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: 1.11.57
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+Version: 1.11.58
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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>
man/cnSetExample.Rd
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+\name{cnSetExample}
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+\alias{cnSetExample}
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+\alias{cnSetExample2}
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+\docType{data}
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+\title{
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+	Object of class 'CNSet'
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+}
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+\description{
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+
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+	The data for the first 16 polymorphic markers in the HapMap analysis.
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+
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+}
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+\details{
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+  This object was created from the copynumber vignette in inst/scripts.
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+}
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+\usage{
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+
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+data(cnSetExample)
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+data(cnSetExample2)
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+
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+}
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+\format{
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+  The data illustrates the \code{CNSet-class}, with
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+	\code{assayData} containing the quantile-normalized
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+	intensities for the A and B alleles, genotype calls and
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+	confidence scores.  New slots that specific to copy number
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+	estimation are \code{batch} and \code{batchStatistics}.
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+
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+}
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+\examples{
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+\dontshow{
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+\dontrun{
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+
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+      ## hapmap phase 3 data
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+      data(hapmapSet, package="CnvScripts")
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+      marker.index <- which(chromosome(hapmapSet) == 8)
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+      marker.index <- marker.index[1:60e3]
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+      sample.CNSet <- hapmapSet[marker.index, c(1168:1169)]
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+      cnSetExample <- sample.CNSet
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+      save(cnSetExample, file="~/Software/crlmm/data/cnSetExample.rda")
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+      ## 2 samples, many markers
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+
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+      ## all samples, a few markers
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+      snp.index <- which(isSnp(hapmapSet))[1:100]
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+      np.index <- which(!isSnp(hapmapSet))[1:100]
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+      marker.index <- c(snp.index, np.index)
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+      sample.CNSet2 <- hapmapSet[marker.index, ]
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+      sample.CNSet2$gender <- sample.CNSet2$gender[]
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+      sample.CNSet2$SKW <- sample.CNSet2$SKW[]
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+      sample.CNSet2$SNR <- sample.CNSet2$SNR[]
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+      cnSetExample2 <- sample.CNSet2
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+      save(cnSetExample2, file="~/Software/crlmm/data/cnSetExample2.rda")
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+}
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+}
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+data(cnSetExample)
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+## --------------------------------------------------
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+## accessors for the feature-level info
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+## --------------------------------------------------
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+chromosome(cnSetExample)[1:5]
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+position(cnSetExample)[1:5]
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+isSnp(cnSetExample)[1:5]
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+table(isSnp(cnSetExample))
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+## --------------------------------------------------
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+## sample-level statistics computed by crlmm
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+## --------------------------------------------------
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+varLabels(cnSetExample)
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+## accessors for sample-level statistics
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+## The signal to noise ratio (SNR)
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+cnSetExample$SNR[]
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+## the skew
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+cnSetExample$SKW[]
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+## the gender (gender is imputed unless specified in the call to crlmm)
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+table(cnSetExample$gender[])  ## 1=male, 2=female
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+## --------------------------------------------------
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+## batchStatistics
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+## -------------------------------------------------- estimate of
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+## intercept from linear model
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+dim(nu(cnSetExample, "A"))
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+## background for the A allele in the 2 batches for the
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+## first 5 markers
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+nu(cnSetExample, "A")[1:5, ]
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+## background for the B allele in the 2 batches for the
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+## first 5 markers
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+nu(cnSetExample, "B")[1:5, ]
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+## the slope
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+phi(cnSetExample, "A")[1:5, ]
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+
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+## --------------------------------------------------
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+## calculating allele-specific copy number
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+## --------------------------------------------------
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+(ca <- CA(cnSetExample, i=1:5, j=1:2))
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+## copy number for allele B, first 5 markers, first 2 samples
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+(cb <- CB(cnSetExample, i=1:5, j=1:2))
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+index <- which(!isSnp(cnSetExample))[1:5]
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+cn2 <- CA(cnSetExample, i=index, j=1:2)
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+## note, cb is 0 at nonpolymorphic loci
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+CB(cnSetExample, i=index, j=1:2)
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+## A shortcut for total copy number
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+cn3 <- totalCopynumber(cnSetExample, i=1:5, j=1:2)
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+all.equal(cn3, ca+cb)
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+cn4 <- totalCopynumber(cnSetExample, i=index, j=1:2)
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+all.equal(cn4, cn2)
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+
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+## markers 1-5, all samples
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+cn5 <- totalCopynumber(cnSetExample, i=1:5)
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+## all markers, samples 1-2
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+cn6 <- totalCopynumber(cnSetExample, j=1:2)
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+}
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+\keyword{datasets}