[Wavetiling-commits] r8 - in pkg: . R

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

Author: ppipeler
Date: 2011-12-12 14:33:29 +0100 (Mon, 12 Dec 2011)
New Revision: 8

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	2011-12-11 21:03:59 UTC (rev 7)
+++ pkg/DESCRIPTION	2011-12-12 13:33:29 UTC (rev 8)
@@ -1,24 +1,20 @@
 Package: waveTiling
-Version: 0.1.1
-Date: 2011-12-05
-License: GPL-2
+Version: 0.1-1
+Date: 2011-12-04
+License: GPL (>=2)
 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: oligoClasses, oligo, Biobase, affy, GenomeGraphs, IRanges, Biostrings, waveslim, methods, preprocessCore, GenomicRanges
-Imports: 
-Suggests: 
+Depends: 
+Imports: oligoClasses, oligo, Biobase, affy, GenomeGraphs, 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
-	  initialize-methods.R
-          helperFunctions.R
-	  methods-mapFilterProbe.R
-	  methods-waveTilingFeatureSet.R
-	  methods-Wfm.R
-	  show-methods.R
-URL:
+Collate: allClasses.R allGenerics.R helperFunctions.R
+        initialize-methods.R methods-mapFilterProbe.R
+        methods-waveTilingFeatureSet.R methods-Wfm.R show-methods.R
+URL: https://r-forge.r-project.org/projects/wavetiling/
 LazyLoad: yes
 LazyData:
 biocViews:
-
+Packaged: 2011-12-05 20:18:51 UTC; kdebeuf

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2011-12-11 21:03:59 UTC (rev 7)
+++ pkg/NAMESPACE	2011-12-12 13:33:29 UTC (rev 8)
@@ -49,7 +49,7 @@
 ## exportMethods(show)
 
 ## waveTilingFeatureSet methods
-exportMethods(addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap,                      selectProbesFromTilingFeatureSet, bgCorrQn, makeDesign, wfm.analysis)
+exportMethods(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	2011-12-11 21:03:59 UTC (rev 7)
+++ pkg/R/allGenerics.R	2011-12-12 13:33:29 UTC (rev 8)
@@ -1,11 +1,13 @@
 # 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, ...)
 {
 	standardGeneric("filterOverlap")

Modified: pkg/R/initialize-methods.R
===================================================================
--- pkg/R/initialize-methods.R	2011-12-11 21:03:59 UTC (rev 7)
+++ pkg/R/initialize-methods.R	2011-12-12 13:33:29 UTC (rev 8)
@@ -57,38 +57,39 @@
 #waveTilingFeatureSet
 setMethod("initialize","waveTilingFeatureSet",function (.Object, ...)
 {
-    .local <- function (.Object, assayData, phenoData, ...)
-    {
-        mySlots <- slotNames(.Object)
-        dotArgs <- list(...)
-        isSlot <- names(dotArgs) %in% mySlots
-        if (missing(assayData)) {
-            assayData <- do.call(assayDataNew, dotArgs[!isSlot],
-                envir = parent.frame())
-        }
-        if (missing(phenoData)) {
-            phenoData <- annotatedDataFrameFrom(assayData, byrow = FALSE)
-        }
-        if (is.null(varMetadata(phenoData)[["channel"]])) {
-            varMetadata(phenoData)[["channel"]] <- factor(rep("_ALL_",
-                nrow(varMetadata(phenoData))), levels = c(assayDataElementNames(assayData),
-                "_ALL_"))
-        }
-        appl <- if (storageMode(assayData) == "list")
-            lapply
-        else eapply
-        assaySampleNames <- appl(assayData, function(elt) {
-            cnames <- colnames(elt)
-            if (is.null(cnames))
-                sampleNames(phenoData)
-            else cnames
-        })
-        sampleNames(assayData) <- assaySampleNames
-        sampleNames(phenoData) <- sampleNames(assayData)
-        do.call(callNextMethod, c(.Object, assayData = assayData,
-            phenoData = phenoData, dotArgs[isSlot]))
-    }
-    .local(.Object, ...)
+#    .local <- function (.Object, assayData, phenoData, ...)
+#    {
+#        mySlots <- slotNames(.Object)
+#        dotArgs <- list(...)
+#        isSlot <- names(dotArgs) %in% mySlots
+#        if (missing(assayData)) {
+#            assayData <- do.call(assayDataNew, dotArgs[!isSlot],
+#                envir = parent.frame())
+#        }
+#        if (missing(phenoData)) {
+#            phenoData <- annotatedDataFrameFrom(assayData, byrow = FALSE)
+#        }
+#        if (is.null(varMetadata(phenoData)[["channel"]])) {
+#            varMetadata(phenoData)[["channel"]] <- factor(rep("_ALL_",
+#                nrow(varMetadata(phenoData))), levels = c(assayDataElementNames(assayData),
+#                "_ALL_"))
+#        }
+#        appl <- if (storageMode(assayData) == "list")
+#            lapply
+#        else eapply
+#        assaySampleNames <- appl(assayData, function(elt) {
+#            cnames <- colnames(elt)
+#            if (is.null(cnames))
+#                sampleNames(phenoData)
+#            else cnames
+#        })
+#        sampleNames(assayData) <- assaySampleNames
+#        sampleNames(phenoData) <- sampleNames(assayData)
+#        do.call(callNextMethod, c(.Object, assayData = assayData,
+#            phenoData = phenoData, dotArgs[isSlot]))
+#    }
+#    .local(.Object, ...)
+	callNextMethod(.Object);
 }
 )
 

Modified: pkg/R/methods-waveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-waveTilingFeatureSet.R	2011-12-11 21:03:59 UTC (rev 7)
+++ pkg/R/methods-waveTilingFeatureSet.R	2011-12-12 13:33:29 UTC (rev 8)
@@ -1,4 +1,5 @@
-setMethod("addPheno",signature("waveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)
+#setMethod("addPheno",signature("waveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)
+setReplaceMethod("addPheno",signature("waveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)
 {
 	if (dim(object)[2] != sum(replics))
 	{