[Wavetiling-commits] r12 - in pkg: . R

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

Author: kdbeuf
Date: 2011-12-13 15:31:39 +0100 (Tue, 13 Dec 2011)
New Revision: 12

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


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-12-13 12:23:18 UTC (rev 11)
+++ pkg/DESCRIPTION	2011-12-13 14:31:39 UTC (rev 12)
@@ -1,18 +1,18 @@
 Package: waveTiling
-Version: 0.1-1
+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: 
+Depends: affxparser, oligo
 Imports: oligoClasses, oligo, Biobase, affy, GenomeGraphs, IRanges,
-        Biostrings, waveslim, methods
+        Biostrings, waveslim, methods, affxparser
 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
         initialize-methods.R methods-mapFilterProbe.R
-        methods-waveTilingFeatureSet.R methods-Wfm.R show-methods.R
+        methods-WaveTilingFeatureSet.R methods-Wfm.R show-methods.R
 URL: https://r-forge.r-project.org/projects/wavetiling/
 LazyLoad: yes
 LazyData:

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2011-12-13 12:23:18 UTC (rev 11)
+++ pkg/NAMESPACE	2011-12-13 14:31:39 UTC (rev 12)
@@ -8,6 +8,10 @@
 ## Classes from oligoClasses
 importClassesFrom(oligoClasses, TilingFeatureSet, FeatureSet)
 
+### oligo
+## importFrom(oligo, list.celfiles)
+
+
 ## Classes from Biobase
 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
                   NChannelSet, Versions, VersionedBiobase, Versioned)
@@ -44,7 +48,7 @@
 ## Exporting
 
 ## Classes
-exportClasses(waveTilingFeatureSet, mapFilterProbe, genomeInfo, Wfm)
+exportClasses(WaveTilingFeatureSet, mapFilterProbe, genomeInfo, Wfm)
 
 ## exportMethods(show)
 

Modified: pkg/R/helperFunctions.R
===================================================================
--- pkg/R/helperFunctions.R	2011-12-13 12:23:18 UTC (rev 11)
+++ pkg/R/helperFunctions.R	2011-12-13 14:31:39 UTC (rev 12)
@@ -1,10 +1,3 @@
-## load libraries
-library(oligo)
-library(waveslim)
-library(GenomeGraphs)
-library(preprocessCore)
-library(affy)
-library(Biostrings)
 
 ## functions for data input
 

Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R	2011-12-13 12:23:18 UTC (rev 11)
+++ pkg/R/methods-WaveTilingFeatureSet.R	2011-12-13 14:31:39 UTC (rev 12)
@@ -32,7 +32,7 @@
 {
 	if ((names(pData(object))[1]!="group")|((names(pData(object))[2]!="replicate")))
 	{
-		stop("phenoData of TilingFeatureSet object is not correct. Use 'addPheno()' first.")
+		stop("phenoData of WaveTilingFeatureSet object is not correct. Use 'addPheno()' first.")
 	}
 	noGroups <- length(table(pData(object)$group))
 	return(noGroups)
@@ -54,7 +54,7 @@
 {
 	if ((names(pData(object))[1]!="group")|((names(pData(object))[2]!="replicate")))
 	{
-		stop("phenoData of TilingFeatureSet object is not correct. Use 'addPheno()' first.")
+		stop("phenoData of WaveTilingFeatureSet object is not correct. Use 'addPheno()' first.")
 	}
 	# keep the order safe
 	orderHlp <- order(unique(pData(object)$group))
@@ -66,9 +66,9 @@
 
 setMethod("filterOverlap",signature("WaveTilingFeatureSet"),function(object,remap=TRUE,fastaFile,chrId,strand=c("forward","reverse","both"),MM=FALSE)
 {
-	if (class(object)!="waveTilingFeatureSet")
+	if (class(object)!="WaveTilingFeatureSet")
 	{
-		stop("class of object is not TilingFeatureSet.")
+		stop("class of object is not WaveTilingFeatureSet.")
 	}
 	pmIndex <- oligo::pmindex(object)
 	dataPMSeq <- pmSequence(object)
@@ -351,7 +351,7 @@
 # construct filtered data set
 	if ((names(pData(object))[1]!="group")|((names(pData(object))[2]!="replicate")))
 	{
-		stop("phenoData of TilingFeatureSet object is not correct. Use 'addPheno()' first.")
+		stop("phenoData of WaveTilingFeatureSet object is not correct. Use 'addPheno()' first.")
 	}
 	
 	if (!is.null(filter.overlap))