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
Showing4 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: 1.11.30
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+Version: 1.11.31
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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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@@ -10,7 +10,7 @@ License: Artistic-2.0
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 Depends: R (>= 2.13.0),
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          methods,
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          Biobase (>= 2.11.9),
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-         oligoClasses (>= 1.15.31)
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+         oligoClasses (>= 1.15.40)
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 Imports: affyio (>= 1.19.2),
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          ellipse,
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          ff (>= 2.2-1),
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@@ -34,6 +34,7 @@ Collate: AllGenerics.R
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 	 methods-CNSetLM.R
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 	 methods-eSet.R
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          methods-SnpSuperSet.R
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+	 methods-PredictionRegion.R
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          cnrma-functions.R
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 	 cnset-accessors.R
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          crlmm-functions.R
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@@ -28,7 +28,8 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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 		  chromosome, position, A, B,
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 		  "A<-", "B<-", open, close, flags,
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 		  openff, closeff,
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-		  batchStatistics, "batchStatistics<-", updateObject)
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+		  batchStatistics, "batchStatistics<-", updateObject,
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+		  order, checkOrder)
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 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
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            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
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@@ -65,3 +66,4 @@ export(crlmm,
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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, xyplot)
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 export(ABpanel, constructInf, preprocessInf, genotypeInf)
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+exportClasses(PredictionRegion)
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@@ -1,3 +1,4 @@
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 setOldClass("ellipse")
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 setOldClass("ffdf")
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 setClassUnion("ff_or_matrix", c("ffdf", "ff_matrix", "matrix"))
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+setClass("PredictionRegion", contains="list")
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new file mode 100644
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@@ -0,0 +1,45 @@
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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}