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
Showing1 changed files
... ...
@@ -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.
Browse code

Simplify accessors for batch summaries: Ns, corr, medians, mads

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58646 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:48:38
Showing1 changed files
... ...
@@ -27,7 +27,7 @@ posteriorProbability(object, predictRegion, copyNumber = 0:4, w)
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   \item{w}{ numeric vector of prior probabilities for each of the copy
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     number states.  Must be the same length as \code{copyNumber} and sum
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-    to 1.
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+    to 1.}
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 }
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 \details{
Browse code

Fix usage in Rd files for posterior means and posterior probabilities

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58645 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:48:31
Showing1 changed files
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@@ -10,7 +10,7 @@
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 }
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 \usage{
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-posteriorProbability(object, predictRegion, copyNumber = 0:4)
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+posteriorProbability(object, predictRegion, copyNumber = 0:4, w)
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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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@@ -23,7 +23,12 @@ posteriorProbability(object, predictRegion, copyNumber = 0:4)
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 }
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   \item{copyNumber}{
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     Integer vector.
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-}
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+  }
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+
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+  \item{w}{ numeric vector of prior probabilities for each of the copy
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+    number states.  Must be the same length as \code{copyNumber} and sum
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+    to 1.
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+
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 }
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 \details{
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Browse code

Update help files for posteriorProbability and calculatePosteriorMean

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58640 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:53
Showing1 changed files
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@@ -49,6 +49,11 @@ 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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 dim(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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 }
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 % Add one or more standard keywords, see file 'KEYWORDS' in the
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 % R documentation directory.
Browse code

Add examples for calculatePosteriorMean and posteriorProbability help files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58634 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:17
Showing1 changed files
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@@ -45,6 +45,10 @@ R. Scharpf
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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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+dim(pp)
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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.
Browse code

Add Rd files for calculatePosteriorMean, genotypes, posteriorProbability, and predictionRegion

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58631 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:46:59
Showing1 changed files
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new file mode 100644
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@@ -0,0 +1,51 @@
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+\name{posteriorProbability}
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+\alias{posteriorProbability}
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+\alias{posteriorProbability,CNSet-method}
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+%- Also NEED an '\alias' for EACH other topic documented here.
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+\title{Calculate the posterior probability for integer copy numbers.}
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+
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+\description{
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+  Calculate the posterior probability for integer copy numbers using the
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+  bivariate normal prediction regions.
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+}
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+
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+\usage{
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+posteriorProbability(object, predictRegion, 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{predictRegion}{
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+    A list containing the bivariate normal prediction region for each of
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+    the possible genotypes.
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+}
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+  \item{copyNumber}{
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+    Integer vector.
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+}
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+}
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+\details{
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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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+
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+\author{
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+R. Scharpf
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+}
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+\note{
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+  %Remark about nonpolymorphic probes
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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{genotypes}}, \code{\link{calculatePosteriorMean}}
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+}
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+\examples{
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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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\ No newline at end of file