[Wavetiling-commits] r14 - in pkg: . R

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

Author: ppipeler
Date: 2011-12-13 16:37:21 +0100 (Tue, 13 Dec 2011)
New Revision: 14

Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/allGenerics.R
   pkg/R/initialize-methods.R
   pkg/R/methods-WaveTilingFeatureSet.R
Log:


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-12-13 14:32:26 UTC (rev 13)
+++ pkg/DESCRIPTION	2011-12-13 15:37:21 UTC (rev 14)
@@ -5,9 +5,8 @@
 Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
 Author: Kristof De Beuf <kristof.debeuf at UGent.be>, Peter Pipelers <peter.pipelers at ugent.be> and Lieven Clement <lieven.clement at gmail.com>
 Maintainer: Kristof De Beuf <kristof.debeuf at UGent.be>
-Depends: 
-Imports: oligoClasses, oligo, Biobase, affy, GenomeGraphs, IRanges,
-        Biostrings, waveslim, methods
+Depends: oligoClasses, Biobase, GenomeGraphs 
+Imports: oligo, affy, IRanges, Biostrings, waveslim, methods
 Suggests:
 Description: This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.
 Collate: allClasses.R allGenerics.R helperFunctions.R

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2011-12-13 14:32:26 UTC (rev 13)
+++ pkg/NAMESPACE	2011-12-13 15:37:21 UTC (rev 14)
@@ -2,8 +2,6 @@
 
 ## Importing
 importClassesFrom(methods, ANY, character, data.frame, "function", integer, matrix,                     numeric)
-importMethodsFrom(methods, initialize, show)
-importFrom(methods, "@<-", callNextMethod, new, validObject)
 
 ## Classes from oligoClasses
 importClassesFrom(oligoClasses, TilingFeatureSet, FeatureSet)
@@ -12,6 +10,11 @@
 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
                   NChannelSet, Versions, VersionedBiobase, Versioned)
 
+importMethodsFrom(methods, initialize, show)
+importFrom(methods, "@<-", callNextMethod, new, validObject)
+
+
+
 ## Classes from GenomeGraphs
 importClassesFrom(GenomeGraphs, DisplayPars, GenericArray, MappedRead, BaseTrack,                       Legend, Title, Gene, Transcript, GenomeAxis, ExonArray,  gdObject,                    Overlay, RectangleOverlay, TextOverlay, AnnotationTrack,                              Segmentation, TrackOverlay)
 
@@ -41,6 +44,7 @@
 ## Methods from oligo
 ## importMethodsFrom(oligo, ...)
 
+
 ## Exporting
 
 ## Classes
@@ -49,7 +53,7 @@
 ## exportMethods(show)
 
 ## waveTilingFeatureSet methods
-exportMethods(getNoGroups, getGroupNames, getReplics, filterOverlap,                      selectProbesFromTilingFeatureSet, bgCorrQn, makeDesign, wfm.analysis)
+exportMethods( addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap,                      selectProbesFromTilingFeatureSet, bgCorrQn, makeDesign, wfm.analysis)
 
 ## mapFilterProbe methods
 exportMethods(getFilteredIndices, getChromosome, getPosition, getStrand,                            selectProbesFromFilterOverlap)

Modified: pkg/R/allGenerics.R
===================================================================
--- pkg/R/allGenerics.R	2011-12-13 14:32:26 UTC (rev 13)
+++ pkg/R/allGenerics.R	2011-12-13 15:37:21 UTC (rev 14)
@@ -1,12 +1,11 @@
 # method data extraction
 
-#setGeneric("addPheno",function(object, noGroups, groupNames, replics, ...)
-#{
-#	standardGeneric("addPheno")
-#}
-#)
+setGeneric("addPheno",function(object, noGroups, groupNames, replics, ...)
+{
+	standardGeneric("addPheno")
+}
+)
 
-setGeneric("addPheno<-",function(object,noGroups,groupNames,replics,...){standardGeneric ("addPheno<-")})
 
 setGeneric("filterOverlap",function(object, remap=TRUE, fastaFile, chrId,  strand=c("forward","reverse","both"), MM=FALSE, ...)
 {

Modified: pkg/R/initialize-methods.R
===================================================================
--- pkg/R/initialize-methods.R	2011-12-13 14:32:26 UTC (rev 13)
+++ pkg/R/initialize-methods.R	2011-12-13 15:37:21 UTC (rev 14)
@@ -54,7 +54,7 @@
 })
 
 #waveTilingFeatureSet
-setMethod("initialize","waveTilingFeatureSet",function (.Object, ...)
+setMethod("initialize","WaveTilingFeatureSet",function (.Object, ...)
 {
 	callNextMethod(.Object);
 }

Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R	2011-12-13 14:32:26 UTC (rev 13)
+++ pkg/R/methods-WaveTilingFeatureSet.R	2011-12-13 15:37:21 UTC (rev 14)
@@ -1,4 +1,4 @@
-setReplaceMethod("addPheno",signature("WaveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)
+setMethod("addPheno",signature("WaveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)
 {
 	if (dim(object)[2] != sum(replics))
 	{