Browse code

merge collab branch

* collab:
update vignettes/Makefile
update .gitignore
update table in CopyNumberViewiew
bump dependency on oligoClasses version
Update alias for "[" method for PredictionRegion objects
Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch. The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:49:34
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 \Rdversion{1.1}
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 \docType{class}
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 \alias{PredictionRegion-class}
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-\alias{[,PredictionRegion-method}
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+\alias{[,PredictionRegion,ANY,ANY,ANY-method}
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 \title{Class \code{"PredictionRegion"}}
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 \description{
Browse code

Add PredictionRegion class that contains 'list'. Export in NAMESPACE. predictionRegion returns PredictionRegion class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58653 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:49:20
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+\name{PredictionRegion-class}
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+\Rdversion{1.1}
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+\docType{class}
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+\alias{PredictionRegion-class}
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+\alias{[,PredictionRegion-method}
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+
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+\title{Class \code{"PredictionRegion"}}
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+\description{
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+  A container for bivariate normal prediction regions for SNP data and
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+  univarite prediction regions for nonpolymorphic markers.
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+}
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+\section{Objects from the Class}{
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+  Objects from the class are created from the \code{predictionRegion} function.
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+}
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+\section{Slots}{
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+  \describe{
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+    \item{\code{.Data}:}{Object of class \code{"list"} ~~ }
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+  }
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+}
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+\section{Extends}{
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+Class \code{"\linkS4class{list}"}, from data part.
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+Class \code{"\linkS4class{vector}"}, by class "list", distance 2.
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+Class \code{"\linkS4class{AssayData}"}, by class "list", distance 2.
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+Class \code{"\linkS4class{list_or_ffdf}"}, by class "list", distance 2.
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+Class \code{vectorORfactor}, by class "list", distance 3.
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+}
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+\section{Methods}{
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+  \describe{
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+    \item{[}{\code{signature(x = "PredictionRegion")}: ... } Prediction
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+    regions can be subset by markers.
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+	 }
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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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+\seealso{
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+\code{\link{predictionRegion}}
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+}
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+\examples{
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+showClass("PredictionRegion")
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+}
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+\keyword{classes}