Browse code

Do not export calculatePosteriorMean

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59038 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/10/2011 12:17:35
Showing6 changed files

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@@ -1,7 +1,7 @@
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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: 1.11.54
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+Version: 1.11.55
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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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@@ -67,7 +67,7 @@ export(crlmm,
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        genotype.Illumina,
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        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
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 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
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-exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
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+exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
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 	      xyplot, calculateRBaf)
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 export(ABpanel, constructInf, preprocessInf, genotypeInf)
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 exportClasses(PredictionRegion)
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deleted file mode 100644
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@@ -1,65 +0,0 @@
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-\name{calculatePosteriorMean}
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-\alias{calculatePosteriorMean}
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-\alias{calculatePosteriorMean,CNSet-method}
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-%- Also NEED an '\alias' for EACH other topic documented here.
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-\title{Calculate the posterior mean of the integer copy numbers}
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-\description{
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-
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-  Computes the posterior mean copy number from the bivariate normal
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-  prediction regions.
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-
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-}
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-
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-\usage{
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-calculatePosteriorMean(object, posteriorProb, copyNumber = 0:4, ...)
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-}
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-%- maybe also 'usage' for other objects documented here.
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-\arguments{
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-  \item{object}{
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-    A \code{CNSet} object.
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-}
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-  \item{posteriorProb}{
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-    The posterior probability for copy numbers 0-4.
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-  }
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-
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-  \item{copyNumber}{
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-    Integer vector.
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-}
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-  \item{\dots}{
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-    Ignored
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-}
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-}
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-\details{
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-}
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-\value{
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-  An array  (features x samples x copy number)
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-}
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-
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-\author{
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-R. Scharpf
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-}
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-
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-
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-%% ~Make other sections like Warning with \section{Warning }{....} ~
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-
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-\seealso{
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-  \code{\link{predictionRegion}}, \code{\link{posteriorProbability}}
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-}
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-\examples{
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-data(sample.CNSet)
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-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)
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-pp <- posteriorProbability(sample.CNSet, predictRegion=pr)
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-pm <- calculatePosteriorMean(sample.CNSet, posteriorProb=pp)
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-
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-## multiple batches
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-data(sample.CNSet2)
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-pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)
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-pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)
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-## prediction regions not available for some batches
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-pm <- calculatePosteriorMean(sample.CNSet2, posteriorProb=pp)
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-
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-}
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-% Add one or more standard keywords, see file 'KEYWORDS' in the
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-% R documentation directory.
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-\keyword{array}
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-\keyword{models}
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@@ -30,9 +30,11 @@ posteriorProbability(object, predictRegion, copyNumber = 0:4, w)
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     to 1.}
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 }
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-\details{
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+\details{
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+This is currently under development.
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 }
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+
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 \value{
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 An array (features x samples x copy number)
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 }
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@@ -40,25 +42,26 @@ An array (features x samples x copy number)
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 \author{
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 R. Scharpf
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 }
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+
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 \note{
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-  %Remark about nonpolymorphic probes
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+  This is under development. Use at your own risk.
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 }
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 %% ~Make other sections like Warning with \section{Warning }{....} ~
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 \seealso{
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-  \code{\link{predictionRegion}}, \code{\link{genotypes}}, \code{\link{calculatePosteriorMean}}
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+  \code{\link{predictionRegion}}, \code{\link{genotypes}} %\code{\link{calculatePosteriorMean}}
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 }
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 \examples{
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-data(sample.CNSet)
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-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)
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-pp <- posteriorProbability(sample.CNSet, predictRegion=pr)
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+data(cnSetExample)
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+pr <- predictionRegion(cnSetExample, copyNumber=0:4)
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+pp <- posteriorProbability(cnSetExample, predictRegion=pr)
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 dim(pp)
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 ## multiple batches
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-data(sample.CNSet2)
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-pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)
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-pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)
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+data(cnSetExample2)
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+pr <- predictionRegion(cnSetExample2, copyNumber=0:4)
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+pp <- posteriorProbability(cnSetExample2, predictRegion=pr)
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 }
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 % Add one or more standard keywords, see file 'KEYWORDS' in the
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 % R documentation directory.
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@@ -54,12 +54,12 @@ predictionRegion(object, copyNumber)
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 %% ~Make other sections like Warning with \section{Warning }{....} ~
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 \seealso{
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-  \code{\link{calculatePosteriorMean}},
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+%  \code{\link{calculatePosteriorMean}},
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   \code{\link{posteriorProbability}}, \code{\link{genotypes}}
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 }
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 \examples{
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-data(sample.CNSet)
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-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)
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+data(cnSetExample)
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+pr <- predictionRegion(cnSetExample, copyNumber=0:4)
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 names(pr)
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 ## bivariate normal prediction region for NULL genotype (homozygous deletion)
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 str(pr[["NULL"]])
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deleted file mode 100644
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-\name{sample.CNSet}
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-\alias{sample.CNSet}
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-\alias{sample.CNSet2}
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-\alias{cnSet}
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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(sample.CNSet)
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-data(sample.CNSet2)
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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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-      ## 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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-}
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-}
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-data(sample.CNSet)
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-## --------------------------------------------------
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-## accessors for the feature-level info
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-## --------------------------------------------------
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-chromosome(sample.CNSet)[1:5]
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-position(sample.CNSet)[1:5]
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-isSnp(sample.CNSet)[1:5]
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-table(isSnp(sample.CNSet))
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-## --------------------------------------------------
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-## sample-level statistics computed by crlmm
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-## --------------------------------------------------
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-varLabels(sample.CNSet)
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-## accessors for sample-level statistics
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-## The signal to noise ratio (SNR)
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-sample.CNSet$SNR[]
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-## the skew
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-sample.CNSet$SKW[]
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-## the gender (gender is imputed unless specified in the call to crlmm)
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-table(sample.CNSet$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(sample.CNSet, "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(sample.CNSet, "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(sample.CNSet, "B")[1:5, ]
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-## the slope
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-phi(sample.CNSet, "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(sample.CNSet, 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(sample.CNSet, i=1:5, j=1:2))
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-index <- which(!isSnp(sample.CNSet))[1:5]
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-cn2 <- CA(sample.CNSet, i=index, j=1:2)
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-## note, cb is 0 at nonpolymorphic loci
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-CB(sample.CNSet, i=index, j=1:2)
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-## A shortcut for total copy number
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-cn3 <- totalCopynumber(sample.CNSet, i=1:5, j=1:2)
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-all.equal(cn3, ca+cb)
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-cn4 <- totalCopynumber(sample.CNSet, 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(sample.CNSet, i=1:5)
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-## all markers, samples 1-2
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-cn6 <- totalCopynumber(sample.CNSet, j=1:2)
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-}
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-\keyword{datasets}