@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.11.54

+Version: 1.11.55

 Date: 2010-12-10

 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

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -67,7 +67,7 @@ export(crlmm,

        genotype.Illumina,

        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)

 export(genotypes, totalCopynumber, rawCopynumber, xyplot)

-exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,

+exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,

 	      xyplot, calculateRBaf)

 export(ABpanel, constructInf, preprocessInf, genotypeInf)

 exportClasses(PredictionRegion)

deleted file mode 100644

@@ -1,65 +0,0 @@

-\name{calculatePosteriorMean}

-\alias{calculatePosteriorMean}

-\alias{calculatePosteriorMean,CNSet-method}

-%- Also NEED an '\alias' for EACH other topic documented here.

-\title{Calculate the posterior mean of the integer copy numbers}

-\description{

-

-  Computes the posterior mean copy number from the bivariate normal

-  prediction regions.

-

-}

-

-\usage{

-calculatePosteriorMean(object, posteriorProb, copyNumber = 0:4, ...)

-}

-%- maybe also 'usage' for other objects documented here.

-\arguments{

-  \item{object}{

-    A \code{CNSet} object.

-}

-  \item{posteriorProb}{

-    The posterior probability for copy numbers 0-4.

-  }

-

-  \item{copyNumber}{

-    Integer vector.

-}

-  \item{\dots}{

-    Ignored

-}

-}

-\details{

-}

-\value{

-  An array  (features x samples x copy number)

-}

-

-\author{

-R. Scharpf

-}

-

-

-%% ~Make other sections like Warning with \section{Warning }{....} ~

-

-\seealso{

-  \code{\link{predictionRegion}}, \code{\link{posteriorProbability}}

-}

-\examples{

-data(sample.CNSet)

-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)

-pp <- posteriorProbability(sample.CNSet, predictRegion=pr)

-pm <- calculatePosteriorMean(sample.CNSet, posteriorProb=pp)

-

-## multiple batches

-data(sample.CNSet2)

-pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)

-pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)

-## prediction regions not available for some batches

-pm <- calculatePosteriorMean(sample.CNSet2, posteriorProb=pp)

-

-}

-% Add one or more standard keywords, see file 'KEYWORDS' in the

-% R documentation directory.

-\keyword{array}

-\keyword{models}

@@ -30,9 +30,11 @@ posteriorProbability(object, predictRegion, copyNumber = 0:4, w)

     to 1.}

 }

-\details{

+\details{

+This is currently under development.

 }

+

 \value{

 An array (features x samples x copy number)

 }

@@ -40,25 +42,26 @@ An array (features x samples x copy number)

 \author{

 R. Scharpf

 }

+

 \note{

-  %Remark about nonpolymorphic probes

+  This is under development. Use at your own risk.

 }

 %% ~Make other sections like Warning with \section{Warning }{....} ~

 \seealso{

-  \code{\link{predictionRegion}}, \code{\link{genotypes}}, \code{\link{calculatePosteriorMean}}

+  \code{\link{predictionRegion}}, \code{\link{genotypes}} %\code{\link{calculatePosteriorMean}}

 }

 \examples{

-data(sample.CNSet)

-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)

-pp <- posteriorProbability(sample.CNSet, predictRegion=pr)

+data(cnSetExample)

+pr <- predictionRegion(cnSetExample, copyNumber=0:4)

+pp <- posteriorProbability(cnSetExample, predictRegion=pr)

 dim(pp)

 ## multiple batches

-data(sample.CNSet2)

-pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)

-pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)

+data(cnSetExample2)

+pr <- predictionRegion(cnSetExample2, copyNumber=0:4)

+pp <- posteriorProbability(cnSetExample2, predictRegion=pr)

 }

 % Add one or more standard keywords, see file 'KEYWORDS' in the

 % R documentation directory.

@@ -54,12 +54,12 @@ predictionRegion(object, copyNumber)

 %% ~Make other sections like Warning with \section{Warning }{....} ~

 \seealso{

-  \code{\link{calculatePosteriorMean}},

+%  \code{\link{calculatePosteriorMean}},

   \code{\link{posteriorProbability}}, \code{\link{genotypes}}

 }

 \examples{

-data(sample.CNSet)

-pr <- predictionRegion(sample.CNSet, copyNumber=0:4)

+data(cnSetExample)

+pr <- predictionRegion(cnSetExample, copyNumber=0:4)

 names(pr)

 ## bivariate normal prediction region for NULL genotype (homozygous deletion)

 str(pr[["NULL"]])

deleted file mode 100644

@@ -1,103 +0,0 @@

-\name{sample.CNSet}

-\alias{sample.CNSet}

-\alias{sample.CNSet2}

-\alias{cnSet}

-\docType{data}

-\title{

-	Object of class 'CNSet'

-}

-\description{

-

-	The data for the first 16 polymorphic markers in the HapMap analysis.

-

-}

-\details{

-  This object was created from the copynumber vignette in inst/scripts.

-}

-\usage{

-

-data(sample.CNSet)

-data(sample.CNSet2)

-

-}

-\format{

-  The data illustrates the \code{CNSet-class}, with

-	\code{assayData} containing the quantile-normalized

-	intensities for the A and B alleles, genotype calls and

-	confidence scores.  New slots that specific to copy number

-	estimation are \code{batch} and \code{batchStatistics}.

-

-}

-\examples{

-\dontshow{

-\dontrun{

-

-      ## hapmap phase 3 data

-      data(hapmapSet, package="CnvScripts")

-      marker.index <- which(chromosome(hapmapSet) == 8)

-      marker.index <- marker.index[1:60e3]

-      sample.CNSet <- hapmapSet[marker.index, c(1168:1169)]

-      ## 2 samples, many markers

-

-      ## all samples, a few markers

-      snp.index <- which(isSnp(hapmapSet))[1:100]

-      np.index <- which(!isSnp(hapmapSet))[1:100]

-      marker.index <- c(snp.index, np.index)

-      sample.CNSet2 <- hapmapSet[marker.index, ]

-}

-}

-data(sample.CNSet)

-## --------------------------------------------------

-## accessors for the feature-level info

-## --------------------------------------------------

-chromosome(sample.CNSet)[1:5]

-position(sample.CNSet)[1:5]

-isSnp(sample.CNSet)[1:5]

-table(isSnp(sample.CNSet))

-## --------------------------------------------------

-## sample-level statistics computed by crlmm

-## --------------------------------------------------

-varLabels(sample.CNSet)

-## accessors for sample-level statistics

-## The signal to noise ratio (SNR)

-sample.CNSet$SNR[]

-## the skew

-sample.CNSet$SKW[]

-## the gender (gender is imputed unless specified in the call to crlmm)

-table(sample.CNSet$gender[])  ## 1=male, 2=female

-## --------------------------------------------------

-## batchStatistics

-## -------------------------------------------------- estimate of

-## intercept from linear model

-dim(nu(sample.CNSet, "A"))

-## background for the A allele in the 2 batches for the

-## first 5 markers

-nu(sample.CNSet, "A")[1:5, ]

-## background for the B allele in the 2 batches for the

-## first 5 markers

-nu(sample.CNSet, "B")[1:5, ]

-## the slope

-phi(sample.CNSet, "A")[1:5, ]

-

-## --------------------------------------------------

-## calculating allele-specific copy number

-## --------------------------------------------------

-(ca <- CA(sample.CNSet, i=1:5, j=1:2))

-## copy number for allele B, first 5 markers, first 2 samples

-(cb <- CB(sample.CNSet, i=1:5, j=1:2))

-index <- which(!isSnp(sample.CNSet))[1:5]

-cn2 <- CA(sample.CNSet, i=index, j=1:2)

-## note, cb is 0 at nonpolymorphic loci

-CB(sample.CNSet, i=index, j=1:2)

-## A shortcut for total copy number

-cn3 <- totalCopynumber(sample.CNSet, i=1:5, j=1:2)

-all.equal(cn3, ca+cb)

-cn4 <- totalCopynumber(sample.CNSet, i=index, j=1:2)

-all.equal(cn4, cn2)

-

-## markers 1-5, all samples

-cn5 <- totalCopynumber(sample.CNSet, i=1:5)

-## all markers, samples 1-2

-cn6 <- totalCopynumber(sample.CNSet, j=1:2)

-}

-\keyword{datasets}