[Wavetiling-commits] r20 - in pkg: . R inst inst/doc vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 17 17:31:42 CET 2012
Author: kdbeuf
Date: 2012-02-17 17:31:41 +0100 (Fri, 17 Feb 2012)
New Revision: 20
Added:
pkg/vignettes/
pkg/vignettes/Sweave.sty
pkg/vignettes/waveTiling-vignette.Rnw
Removed:
pkg/inst/example1.R
pkg/inst/example2.R
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/allGenerics.R
pkg/R/helperFunctions.R
pkg/R/methods-WaveTilingFeatureSet.R
pkg/R/methods-WfmFit.R
pkg/R/methods-WfmInf.R
pkg/R/methods-mapFilterProbe.R
pkg/inst/doc/waveTiling-vignette.Rnw
Log:
adapted mapFilterProbe / vignette
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/DESCRIPTION 2012-02-17 16:31:41 UTC (rev 20)
@@ -1,17 +1,17 @@
Package: waveTiling
Version: 0.1.1
-Date: 2011-12-04
+Date: 2012-02-16
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: oligo, oligoClasses, Biobase, GenomeGraphs, IRanges, Biostrings, GenomicRanges, waveslim
-Imports: affy, methods
+Depends: oligo, oligoClasses, Biobase, GenomeGraphs, IRanges, Biostrings, GenomicRanges, waveslim, BSgenome
+Imports: methods, affy, preprocessCore
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-WfmFit.R methods-WfmInf.R show-methods.R
URL: https://r-forge.r-project.org/projects/wavetiling/
LazyLoad: yes
LazyData:
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/NAMESPACE 2012-02-17 16:31:41 UTC (rev 20)
@@ -1,42 +1,32 @@
-useDynLib("waveTiling")
+## useDynLib("waveTiling")
## Importing
importClassesFrom(methods, ANY, character, data.frame, "function", integer, matrix, numeric)
## Classes from oligoClasses
-importClassesFrom(oligoClasses, TilingFeatureSet, FeatureSet)
+## importClassesFrom(oligoClasses, TilingFeatureSet, FeatureSet)
## Classes from Biobase
-importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
- NChannelSet, Versions, VersionedBiobase, Versioned)
+## importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME, NChannelSet, Versions, VersionedBiobase, Versioned)
importMethodsFrom(methods, initialize, show)
importFrom(methods, "@<-", callNextMethod, new, validObject)
+importFrom(preprocessCore, normalize.quantiles)
+importFrom(affy, bg.adjust)
-
## Classes from GenomeGraphs
-importClassesFrom(GenomeGraphs, DisplayPars, GenericArray, MappedRead, BaseTrack, Legend, Title, Gene, Transcript, GenomeAxis, ExonArray, gdObject, Overlay, RectangleOverlay, TextOverlay, AnnotationTrack, Segmentation, TrackOverlay)
+## importClassesFrom(GenomeGraphs, DisplayPars, GenericArray, MappedRead, BaseTrack, Legend, Title, Gene, Transcript, GenomeAxis, ExonArray, gdObject, Overlay, RectangleOverlay, TextOverlay, AnnotationTrack, Segmentation, TrackOverlay)
## Methods from Biobase
-importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
- "annotation<-", assayData, "assayData<-", combine,
- experimentData, "experimentData<-", exprs,
- "exprs<-", featureData, "featureData<-",
- featureNames, fvarLabels, geneNames, pData,
- "pData<-", phenoData, "phenoData<-", sampleNames,
- se.exprs, "se.exprs<-", storageMode,
- "storageMode<-")
+## importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation, "annotation<-", assayData, "assayData<-", combine, experimentData, "experimentData<-", exprs, "exprs<-", featureData, "featureData<-", featureNames, fvarLabels, geneNames, pData, "pData<-", phenoData, "phenoData<-", sampleNames, se.exprs, "se.exprs<-", storageMode, "storageMode<-")
-## Methods from GenomeGraphs
-## importMethodsFrom(GenomeGraphs, gdPlot, DisplayPars, geneRegionBiomart, geneBiomart, makeLegend,makeGene, makeGeneRegion, makeTranscript, makeExonArray, makeGeneModel, makeBaseTrack, makeRectangleOverlay, makeTextOverlay, makeSegmentation, makeSmoothing, makeTitle, makeGenericArray, makeIdeogram, makeGenomeAxis, makeAnnotationTrack)
-
## Methods from Biostrings
-importMethodsFrom(Biostrings, complement)
+## importMethodsFrom(Biostrings, complement)
## Methods from IRanges
-importMethodsFrom(IRanges, subseq)
+## importMethodsFrom(IRanges, subseq)
## Methods from waveslim
## importFrom(waveslim, wave.filter)
@@ -59,13 +49,13 @@
exportMethods(plot)
## waveTilingFeatureSet methods
-exportMethods( addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet, bgCorrQn, makeDesign, wfm.analysis)
+exportMethods(addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet,bgCorrQn,wfm.analysis)
## mapFilterProbe methods
-exportMethods(getFilteredIndices, getChromosome, getPosition, getStrand, selectProbesFromFilterOverlap)
+exportMethods(getFilteredIndices, getPosition, selectProbesFromFilterOverlap)
## WfmFit methods
-exportMethods(getProbePosition, getNoProbes, getBetaMAP, getVarBetaMAP, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getWfmMethod, getDesign, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj, getPrior, getAlpha, getDelta, getTwoSided, getRescale, getSigProbes, getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff, getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions)
+exportMethods(getProbePosition, getNoProbes, getBetaMAP, getVarBetaMAP, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getWfmMethod, getDesign, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj,getPrior, getAlpha, getDelta, getTwoSided, getRescale, getSigProbes,getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff,getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions)
## Other
export(cel2TilingFeatureSet, makeContrasts, makeDesign)
Modified: pkg/R/allGenerics.R
===================================================================
--- pkg/R/allGenerics.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/allGenerics.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -282,12 +282,13 @@
standardGeneric("getZ")
}
)
-setGeneric("plotWfm",function(object, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
-{
- standardGeneric("plotWfm")
-}
-)
+# setGeneric("plotWfm",function(object, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
+# {
+# standardGeneric("plotWfm")
+# }
+# )
+
setGeneric("getSigGenes",function(fit, inf, annoFile)
{
standardGeneric("getSigGenes")
Modified: pkg/R/helperFunctions.R
===================================================================
--- pkg/R/helperFunctions.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/helperFunctions.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -126,10 +126,12 @@
phi <- B
if (eqsmooth)
{
- out <- .C("MAPMARGEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ #out <- .C("MAPMARGEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ out <- .C("MAPMARGEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends))[4:6]
} else
{
- out <- .C("MAPMARG",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ #out <- .C("MAPMARG",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ out <- .C("MAPMARG",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends))[4:6]
}
names(out) <- c("beta_MAP","varbeta_MAP","phi")
dim(out[[1]]) <- c(K,q)
@@ -158,10 +160,12 @@
phi <- B
if (eqsmooth)
{
- out <- .C("MAPMARGIMPEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ #out <- .C("MAPMARGIMPEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ out <- .C("MAPMARGIMPEQSMOOTH",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends))[4:6]
} else
{
- out <- .C("MAPMARGIMP",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ #out <- .C("MAPMARGIMP",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends), PACKAGE = "waveTiling")[4:6]
+ out <- .C("MAPMARGIMP",as.double(D),as.integer(K),as.double(vareps),as.double(B),as.double(varB),as.double(phi),as.double(X),as.double(diag(t(X)%*%X)),as.integer(q),as.integer(N),as.integer(ends))[4:6]
}
names(out) <- c("beta_MAP","varbeta_MAP","phi")
dim(out[[1]]) <- c(K,q)
Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/methods-WaveTilingFeatureSet.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -77,7 +77,7 @@
}
)
-setMethod("filterOverlap",signature("WaveTilingFeatureSet"),function(object,remap=TRUE,fastaFile,chrId,strand=c("forward","reverse","both"),MM=FALSE)
+setMethod("filterOverlap",signature("WaveTilingFeatureSet"),function(object,remap=TRUE,BSgenomeObject,chrId,strand=c("forward","reverse","both"),MM=FALSE)
{
if (!inherits(object,"WaveTilingFeatureSet")) #class(object)!="WaveTilingFeatureSet")
{
@@ -99,16 +99,13 @@
cat("begin remapping forward strand...\n")
cat("extract probe sequences\n")
pmSeqDict <- PDict(dataPMSeq,tb.start=1,tb.end=trBand)
- chrSeqAll <- read.DNAStringSet(fastaFile,format="fasta")
- chrSeq <- chrSeqAll[chrId]
- names(chrSeq) <- paste("chr",chrId,sep="")
cat("match probe sequences to DNA sequence\n")
chrSeqList <- list()
- for (i in 1:length(chrSeq))
+ for (i in chrId)
{
- chrSeqList[[i]] <- chrSeq[[i]]
+ chrSeqList[[i]] <- BSgenomeObject[[i]]
}
- names(chrSeqList) <- names(chrSeq)
+ names(chrSeqList) <- seqnames(BSgenomeObject)[chrId]
startPM <- lapply(chrSeqList,function(x) startIndex(matchPDict(pmSeqDict,x)))
nposChrPM <- lapply(startPM,function(x) sapply(x,length))
pmMatch <- Reduce("+",nposChrPM)==1
@@ -136,15 +133,12 @@
pmSeqDictRevComp <- PDict(dataPMSeqRevComp,tb.start=1,tb.end=trBand)
if (strand=="reverse")
{
- chrSeqAll <- read.DNAStringSet(fastaFile,format="fasta")
- chrSeq <- chrSeqAll[chrId]
- names(chrSeq) <- paste("chr",chrId,sep="")
chrSeqList <- list()
- for (i in 1:length(chrSeq))
+ for (i in chrId)
{
- chrSeqList[[i]] <- chrSeq[[i]]
+ chrSeqList[[i]] <- BSgenomeObject[[i]]
}
- names(chrSeqList) <- names(chrSeq)
+ names(chrSeqList) <- seqnames(BSgenomeObject)[chrId]
}
cat("match probe sequences to DNA sequence\n")
startPMRevComp <- lapply(chrSeqList,function(x) startIndex(matchPDict(pmSeqDictRevComp,x)))
@@ -169,8 +163,8 @@
{
if ((strand=="forward") | (strand=="both"))
{
- pmMatchIndex <- which(pmStrand(object)==1 & pmChr(object) %in% paste("Chr",chrId,sep=""))
- ## Fix me: does not work yet for special chromosomes like Chr C and Chr M in Arabidopsis
+ pmMatchIndex <- which(pmStrand(object)==1 & pmChr(object) %in% seqnames(BSgenomeObject)[chrId])
+ ## Fix me: Is it always capital Chr?
# sometimes 0/1, sometimes +/- ?
chrInit <- pmChr(object)[pmMatchIndex]
posInit <- pmPosition(object)[pmMatchIndex]
@@ -179,7 +173,7 @@
if ((strand=="reverse") | (strand=="both"))
{
dataPMSeqRevComp <- reverseComplement(pmSequence(object))
- pmMatchIndexRevComp <- which(pmStrand(object)==0 & pmChr(object) %in% paste("Chr",chrId,sep=""))
+ pmMatchIndexRevComp <- which(pmStrand(object)==0 & pmChr(object) %in% seqnames(BSgenomeObject)[chrId])
chrInitRevComp <- pmChr(object)[pmMatchIndexRevComp]
posInitRevComp <- pmPosition(object)[pmMatchIndexRevComp]
strandInitRevComp <- pmStrand(object)[pmMatchIndexRevComp]
Modified: pkg/R/methods-WfmFit.R
===================================================================
--- pkg/R/methods-WfmFit.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/methods-WfmFit.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -120,17 +120,17 @@
GlocRegions <- list()
givenDelta <- delta
noGroups <- object at noGroups
- replics<- object at replics
- F<-object at F
- varF<-object at varF
+ replics <- object at replics
+ F <- object at F
+ varF <- object at varF
- P<-ncol(F) ## so P does not need to be stored!
+ P <- ncol(F) ## so P does not need to be stored!
Xsel <- cumsum(replics)-replics+1
X <- object at design.matrix
Xdes <- X[Xsel,]
- Z<-object at Z
+ Z <- object at Z
if (!is.null(contrast.matrix)) {
## Given contrast matrix (CustomFit)
@@ -138,10 +138,10 @@
warning("Custom Inference Procedure Not Implemented yet!")
}
else if (contrasts=="compare") {
- if (inherits(object,"WfmFitFactor") | inherits(object,"WfmFitTime") | inherits(object,"WfmFitCircadian" | inherits(object,"WfmFitCustom"))) {
+ if (inherits(object,"WfmFitFactor") | inherits(object,"WfmFitTime") | inherits(object,"WfmFitCircadian") | inherits(object,"WfmFitCustom")) {
#q <- noGroups*(noGroups-1)/2
q <- noGroups*(noGroups-1)/2
- contr <- makeContrasts(contrasts=contrasts,nlevels=noGroups);
+ contr <- makeContrasts(contrasts=contrasts,nlevels=noGroups);
noBetas <- noGroups
if (is.null(rescale))
{
Modified: pkg/R/methods-WfmInf.R
===================================================================
--- pkg/R/methods-WfmInf.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/methods-WfmInf.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -155,3 +155,4 @@
setMethod("plot",signature=c(fit="WfmFit",inf="WfmInf"),plotWfm)
+
Modified: pkg/R/methods-mapFilterProbe.R
===================================================================
--- pkg/R/methods-mapFilterProbe.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/R/methods-mapFilterProbe.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -36,7 +36,7 @@
{
stop("minPos is greater than maxPos")
}
- selChrom <- (1:length(getFilteredIndices(object)))[getChromosome(object)==paste("chr",as.character(chromosome),sep="")]
+ selChrom <- (1:length(getFilteredIndices(object)))[getChromosome(object)==paste("chr",as.character(chromosome),sep="") | getChromosome(object)==paste("Chr",as.character(chromosome),sep="")]
selStrand <- (1:length(getFilteredIndices(object)))[getStrand(object)==strand]
selHlp <- intersect(selChrom,selStrand)
selPos <- (1:length(getFilteredIndices(object)))[(getPosition(object)>=minPos)&(getPosition(object)<=maxPos)]
Modified: pkg/inst/doc/waveTiling-vignette.Rnw
===================================================================
--- pkg/inst/doc/waveTiling-vignette.Rnw 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/inst/doc/waveTiling-vignette.Rnw 2012-02-17 16:31:41 UTC (rev 20)
@@ -33,6 +33,7 @@
\begin{document}
\maketitle
+\tableofcontents
<<options,echo=FALSE>>=
options(width=72)
@@ -40,6 +41,11 @@
\section{Introduction}
-In this \waveTiling{} package vignette the package's main functionalities to conduct a tiling array trancriptome analysis are illustrated. The implemented method is based on a wavelet-based functional model introduced in [REF] Clement et al. (2012).
+In this \waveTiling{} package vignette the package's main functionalities to conduct a tiling array trancriptome analysis are illustrated. The package contains an implementation of the basic wavelet-based functional model introduced in [REF] Clement et al. (2012), and its extensions towards more complex designs described in [REF] De Beuf et al. (2012). The leaf development data set [REF] (Andriankaja et al., 2012) contains genome-wide expression data measured for six developmental time points (day 8 to day 13) on the plant species \textit{Arabidopsis thaliana}. The experiment was conducted with AGRONOMICS1 tiling arrays [REF] and contains three biological replicates per time point.
+\section{Read in and prepare data for analysis}
+
+First we have to load the \waveTiling{} package and the \Rpackage{waveTilingData} package...
+
+
\end{document}
Deleted: pkg/inst/example1.R
===================================================================
--- pkg/inst/example1.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/inst/example1.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -1,51 +0,0 @@
-## example - read.celfiles ##
-#############################
-
-data_path = "../data/CEL"
-#data_path <- "/home/kdebeuf/research/tiling/arabidopsis_data"
-exp_names = list.celfiles(data_path)
-dna.e2f.wt=read.celfiles(paste(data_path,exp_names,sep="/"),pkgname="pd.at35b.mr.v04.2.tigrv5")
-
-#dna.e2f.wt is object of class TilingFeatureSet
-class(dna.e2f.wt)
-#[1] "TilingFeatureSet"
-#attr(,"package")
-#[1] "oligoClasses"
-
-##Accessing Data Elements
-#names of the features
-featureNames(dna.e2f.wt)
-#unique sample identifiers
-sampleNames(dna.e2f.wt)
-#column names of the phenotype data
-varLabels(dna.e2f.wt)
-#expression matrix
-exprs(dna.e2f.wt)
-#AnnotatedDataFrame
-phenoData(dna.e2f.wt)
-
-##subsetting
-dna.e2f.wt[1:200,]
-
-##phenoData
-dna.e2f.wt <- pheno(dna.e2f.wt,no.groups=2,replicates=c(3,3),groupnames=c("E2F","WT"),DNAreplicates=1)
-phenoData(dna.e2f.wt)
-pData(dna.e2f.wt)
-
-##useful functions
-#vector with pm indices
-pmindices<-pmindex(dna.e2f.wt);
-#vector with pm sequence
-pmseqs<-pmSequence(dna.e2f.wt);
-#vector with probe feature names
-probens<-probeNames(dna.e2f.wt);
-#vector with chromosome info for all PM probes
-pmchrs<-pmChr(dna.e2f.wt)
-
-##example wavelet mixed model
-pmAllChr<-dna.e2f.wt[pmindices];
-#fit - analysis TDDE, no DNA reference
-pmAllChrModel<-wmm.fit(pmAllChr,analysis="TDDE",verbose=TRUE,n.levels=12,DNAref=FALSE)
-#inference
-pmAllChrInference<-wmm.inference(pmAllChrModel,verbose=TRUE);
-
Deleted: pkg/inst/example2.R
===================================================================
--- pkg/inst/example2.R 2012-02-16 07:00:30 UTC (rev 19)
+++ pkg/inst/example2.R 2012-02-17 16:31:41 UTC (rev 20)
@@ -1,44 +0,0 @@
-## example - read.as.FeatureSet ##
-##################################
-
-#data.frame PMchr1_raw
-#create pData
-exprs<-as.matrix(PMchr1_raw[,1:7])
-col1<-c(rep("Case",3),rep("Control",3),rep("DNAref",1))
-col2<-c(rep("E2F",3),rep("WT",3),rep("DNAref",1))
-pData<-data.frame(cbind(col1,col2))
-rownames(pData)<-colnames(exprs)
-colnames(pData)<-c("Type","Group")
-metadata<-data.frame(labelDescription=c("Case/Control Status","Group"),row.names=c("Type","Group"))
-
-tilingExample<-read.as.FeatureSet(exprs=exprs,pkgname="pd.at35b.mr.v04.2.tigrv5",pData=pData,metaData=metadata);
-
-
-#tilingExample is object of class TilingFeatureSet
-class(tilingExample)
-#[1] "TilingFeatureSet"
-#attr(,"package")
-#[1] "oligoClasses"
-
-##Accessing Data Elements
-#names of the features
-featureNames(tilingExample)
-#unique sample identifiers
-sampleNames(tilingExample)
-#column names of the phenotype data
-varLabels(tilingExample)
-#expression matrix
-exprs(tilingExample)
-#AnnotatedDataFrame
-phenoData(tilingExample)
-
-##subsetting
-tilingExample[1:200,]
-
-
-##example wavelet mixed model
-#fit - analysis TDDE, DNA reference available and used in analysis
-pmDNAModel<-wmm.fit(tilingExample,analysis="TDDE",verbose=TRUE,n.levels=12,DNAref=TRUE)
-#inference
-pmDNAInference<-wmm.inference(pmDNAModel,verbose=TRUE);
-
Added: pkg/vignettes/Sweave.sty
===================================================================
--- pkg/vignettes/Sweave.sty (rev 0)
+++ pkg/vignettes/Sweave.sty 2012-02-17 16:31:41 UTC (rev 20)
@@ -0,0 +1,27 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{Sweave}{}
+
+\RequirePackage{ifthen}
+\newboolean{Sweave at gin}
+\setboolean{Sweave at gin}{true}
+\newboolean{Sweave at ae}
+\setboolean{Sweave at ae}{true}
+
+\DeclareOption{nogin}{\setboolean{Sweave at gin}{false}}
+\DeclareOption{noae}{\setboolean{Sweave at ae}{false}}
+\ProcessOptions
+
+\RequirePackage{graphicx,fancyvrb}
+\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
+
+\ifthenelse{\boolean{Sweave at gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
+\ifthenelse{\boolean{Sweave at ae}}{%
+ \RequirePackage[T1]{fontenc}
+ \RequirePackage{ae}
+}{}%
+
+\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
+\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
+
+\newenvironment{Schunk}{}{}
\ No newline at end of file
Added: pkg/vignettes/waveTiling-vignette.Rnw
===================================================================
--- pkg/vignettes/waveTiling-vignette.Rnw (rev 0)
+++ pkg/vignettes/waveTiling-vignette.Rnw 2012-02-17 16:31:41 UTC (rev 20)
@@ -0,0 +1,45 @@
+%\VignetteIndexEntry{The waveTiling package}
+%\VignetteDepends{}
+%\VignetteKeywords{}
+%\VignettePackage{waveTiling}
+\documentclass[10pt]{article}
+
+\usepackage{times}
+\usepackage{hyperref}
+
+\textwidth=6.5in
+\textheight=8.5in
+%\parskip=.3cm
+\oddsidemargin=-.1in
+\evensidemargin=-.1in
+\headheight=-.3in
+
+%\newcommand{\Rfunction}[1]{{\texttt{#1}}}
+%\newcommand{\Robject}[1]{{\texttt{#1}}}
+\newcommand{\Rpackage}[1]{{\textit{#1}}}
+%\newcommand{\Rmethod}[1]{{\texttt{#1}}}
+%\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
+%\newcommand{\Rclass}[1]{{\textit{#1}}}
+%\newcommand{\Rcode}[1]{{\texttt{#1}}}
+
+\newcommand{\software}[1]{\textsf{#1}}
+\newcommand{\R}{\software{R}}
+\newcommand{\waveTiling}{\Rpackage{waveTiling}}
+
+\title{The \waveTiling{} package}
+\author{Kristof De Beuf}
+\date{\today}
+
+\begin{document}
+
+\maketitle
+
+<<options,echo=FALSE>>=
+options(width=72)
+@
+
+\section{Introduction}
+
+In this \waveTiling{} package vignette the package's main functionalities to conduct a tiling array trancriptome analysis are illustrated. The implemented method is based on a wavelet-based functional model introduced in [REF] Clement et al. (2012).
+
+\end{document}
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