[Wavetiling-commits] r25 - in pkg: inst man

[noreply at r-forge.r-project.org]

Author: kdbeuf
Date: 2012-03-02 09:18:23 +0100 (Fri, 02 Mar 2012)
New Revision: 25

Added:
   pkg/man/WaveTilingFeatureSet-class.Rd
   pkg/man/makeContrasts.Rd
Modified:
   pkg/inst/NEWS.Rd
Log:


Modified: pkg/inst/NEWS.Rd
===================================================================
--- pkg/inst/NEWS.Rd	2012-03-01 10:34:01 UTC (rev 24)
+++ pkg/inst/NEWS.Rd	2012-03-02 08:18:23 UTC (rev 25)
@@ -3,6 +3,8 @@
 
 \section{Changes in version x.y}{
   \subsection{NEW FEATURES}{
-    \item ...;
+    \begin{itemize}
+      \item ...;
+    \end{itemize}
   }
 }

Added: pkg/man/WaveTilingFeatureSet-class.Rd
===================================================================
--- pkg/man/WaveTilingFeatureSet-class.Rd	                        (rev 0)
+++ pkg/man/WaveTilingFeatureSet-class.Rd	2012-03-02 08:18:23 UTC (rev 25)
@@ -0,0 +1,65 @@
+\name{WaveTilingFeatureSet-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{WaveTilingFeatureSet-class}
+\alias{initialize,WaveTilingFeatureSet-method}
+\alias{show,WaveTilingFeatureSet-method}
+%\alias{pmStrand,WaveTilingFeatureSet-method}
+\alias{addPheno,WaveTilingFeatureSet-method}
+\alias{bgCorrQn,WaveTilingFeatureSet-method}
+\alias{filterOverlap,WaveTilingFeatureSet-method}
+\alias{getGroupNames,WaveTilingFeatureSet-method}
+\alias{getNoGroups,WaveTilingFeatureSet-method}
+\alias{getReplics,WaveTilingFeatureSet-method}
+\alias{selectProbesFromTilingFeatureSet,WaveTilingFeatureSet-method}
+\alias{wfm.fit,WaveTilingFeatureSet-method}
+
+\title{Class "WaveTilingFeatureSet"}
+
+\description{Class to store expression and phenotypic data from a tiling array experiment, used as input for the wavelet-based transcriptome analysis.}
+
+\section{Objects from the Class}{Objects can be created by calls of the form \code{new("WaveTilingFeatureSet")}.}
+
+\section{Slots}{
+  \describe{
+    \item{\code{manufacturer}:}{Object of class \code{"character"} ~~ }
+    \item{\code{intensityFile}:}{Object of class \code{"character"} ~~ }
+    \item{\code{assayData}:}{Object of class \code{"AssayData"} ~~ }
+    \item{\code{phenoData}:}{Object of class \code{"AnnotatedDataFrame"} ~~ }
+    \item{\code{featureData}:}{Object of class \code{"AnnotatedDataFrame"} ~~ }
+    \item{\code{experimentData}:}{Object of class \code{"MIAME"} ~~ }
+    \item{\code{annotation}:}{Object of class \code{"character"} ~~ }
+    \item{\code{protocolData}:}{Object of class \code{"AnnotatedDataFrame"} ~~ }
+    \item{\code{.__classVersion__}:}{Object of class \code{"Versions"} ~~ }
+  }
+}
+
+\section{Extends}{
+Class \code{"\linkS4class{TilingFeatureSet}"}, directly.
+Class \code{"\linkS4class{FeatureSet}"}, by class "TilingFeatureSet", distance 2.
+Class \code{"\linkS4class{NChannelSet}"}, by class "TilingFeatureSet", distance 3.
+Class \code{"\linkS4class{eSet}"}, by class "TilingFeatureSet", distance 4.
+Class \code{"\linkS4class{VersionedBiobase}"}, by class "TilingFeatureSet", distance 5.
+Class \code{"\linkS4class{Versioned}"}, by class "TilingFeatureSet", distance 6.
+}
+
+\section{Methods}{
+  \describe{
+    \item{addPheno}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{bgCorrQn}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{filterOverlap}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{getGroupNames}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{getNoGroups}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{getReplics}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{selectProbesFromTilingFeatureSet}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+    \item{wfm.fit}{\code{signature(object = "WaveTilingFeatureSet")}: ... }
+	 }
+}
+
+\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
+
+\examples{
+showClass("WaveTilingFeatureSet")
+}
+
+\keyword{classes}

Added: pkg/man/makeContrasts.Rd
===================================================================
--- pkg/man/makeContrasts.Rd	                        (rev 0)
+++ pkg/man/makeContrasts.Rd	2012-03-02 08:18:23 UTC (rev 25)
@@ -0,0 +1,23 @@
+\name{makeContrasts}
+\alias{makeContrasts}
+
+\title{Construct contrast matrix}
+
+\description{Helper function to construct a contrast matrix to be used in the inference procedure of the wavelet-based transcriptome analysis when conducting a pairwise comparison analysis.}
+
+\usage{makeContrasts(contrasts, nlevels)}
+
+\arguments{
+  \item{contrasts}{\code{compare}: contrasts for pairwise comparison analysis.}
+  \item{nlevels}{Number of groups for pairwise comparison analysis.}
+}
+
+\value{numeric matrix}
+
+\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
+
+\examples{
+  makeContrasts(contrasts="compare",nlevels=6)
+}
+
+\keyword{manip}