[Wavetiling-commits] r38 - in pkg: . R inst inst/doc man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 15 11:41:24 CEST 2012
Author: kdbeuf
Date: 2012-05-15 11:41:23 +0200 (Tue, 15 May 2012)
New Revision: 38
Added:
pkg/vignettes/waveTiling-vignette.Rnw
Removed:
pkg/inst/doc/Makefile
pkg/inst/doc/waveTiling-vignette.Rnw
pkg/inst/doc/waveTiling-vignette.pdf
pkg/inst/scripts/
pkg/man/getAlpha.Rd
pkg/man/getBetaWav.Rd
pkg/man/getChromosome.Rd
pkg/man/getDataOrigSpace.Rd
pkg/man/getDataWaveletSpace.Rd
pkg/man/getDelta.Rd
pkg/man/getDesignMatrix.Rd
pkg/man/getEff.Rd
pkg/man/getF.Rd
pkg/man/getFDR.Rd
pkg/man/getFilteredIndices.Rd
pkg/man/getGenomeInfo.Rd
pkg/man/getGenomicRegions.Rd
pkg/man/getGroupNames.Rd
pkg/man/getKj.Rd
pkg/man/getMaxPos.Rd
pkg/man/getMinPos.Rd
pkg/man/getNoGroups.Rd
pkg/man/getNoLevels.Rd
pkg/man/getNoProbes.Rd
pkg/man/getPhenoInfo.Rd
pkg/man/getPosition.Rd
pkg/man/getPrior.Rd
pkg/man/getProbePosition.Rd
pkg/man/getRegions.Rd
pkg/man/getReplics.Rd
pkg/man/getSigProbes.Rd
pkg/man/getSmoothPar.Rd
pkg/man/getStrand.Rd
pkg/man/getTwoSided.Rd
pkg/man/getVarBetaWav.Rd
pkg/man/getVarEff.Rd
pkg/man/getVarEps.Rd
pkg/man/getVarF.Rd
pkg/man/getWaveletFilter.Rd
pkg/vignettes/waveTiling-vignette.pdf
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/allGenerics.R
pkg/R/helperFunctions.R
pkg/man/GenomeInfo-class.Rd
pkg/man/MapFilterProbe-class.Rd
pkg/man/WaveTilingFeatureSet-class.Rd
pkg/man/WfmFit-class.Rd
pkg/man/WfmFitCircadian-class.Rd
pkg/man/WfmFitCustom-class.Rd
pkg/man/WfmFitFactor-class.Rd
pkg/man/WfmFitTime-class.Rd
pkg/man/WfmInf-class.Rd
pkg/man/WfmInfCompare-class.Rd
pkg/man/WfmInfCustom-class.Rd
pkg/man/WfmInfEffects-class.Rd
pkg/man/WfmInfMeans-class.Rd
pkg/man/WfmInfOverallMean-class.Rd
Log:
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/DESCRIPTION 2012-05-15 09:41:23 UTC (rev 38)
@@ -1,13 +1,13 @@
Package: waveTiling
-Version: 0.1.37
-Date: 2012-02-16
+Version: 0.99.0
+Date: 2012-05-14
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, Biostrings
-Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, GenomeGraphs, IRanges
-Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9
+Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
+Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges
+Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling
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
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/NAMESPACE 2012-05-15 09:41:23 UTC (rev 38)
@@ -19,10 +19,10 @@
importMethodsFrom(GenomicRanges, seqnames)
-importMethodsFrom(IRanges, as.matrix, cbind, findOverlaps, ifelse, intersect, lapply, mad, Map, matchMatrix, mean,
- median, ncol, nrow, order, paste, pintersect, pmin,
- queryHits, rbind, reduce, Reduce, Rle, rownames,
- "rownames<-", sapply, stack, start, subjectHits,
+importMethodsFrom(IRanges, as.matrix, cbind, findOverlaps, ifelse, intersect,
+ lapply, mad, Map, mean, median, ncol, nrow, order, paste,
+ pintersect, pmin,queryHits, rbind, reduce, Reduce, Rle,
+ rownames,"rownames<-", sapply, stack, start, subjectHits,
subseq, t, table, tapply, unique, unlist, values,
"values<-", which, width)
@@ -33,10 +33,12 @@
## Import
importFrom(affy, bg.adjust, list.celfiles)
-importFrom(GenomeGraphs, DisplayPars, gdPlot, makeAnnotationTrack,
- makeGenericArray, makeGenomeAxis, makeRectangleOverlay,
- makeTextOverlay)
+importFrom(preprocessCore, normalize.quantiles)
+#importFrom(GenomeGraphs, DisplayPars, gdPlot, makeAnnotationTrack,
+# makeGenericArray, makeGenomeAxis, makeRectangleOverlay,
+# makeTextOverlay)
+
importFrom(GenomicRanges, GRanges, GRangesList)
importFrom(IRanges, IRanges)
Modified: pkg/R/allGenerics.R
===================================================================
--- pkg/R/allGenerics.R 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/R/allGenerics.R 2012-05-15 09:41:23 UTC (rev 38)
@@ -291,7 +291,7 @@
}
)
-setGeneric("plotWfm",function(object, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
+setGeneric("plotWfm",function(fit, inf, annoFile, minPos, maxPos, trackFeature="exon", overlayFeature=c("gene","transposable_element_gene"), two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
{
standardGeneric("plotWfm")
}
Modified: pkg/R/helperFunctions.R
===================================================================
--- pkg/R/helperFunctions.R 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/R/helperFunctions.R 2012-05-15 09:41:23 UTC (rev 38)
@@ -374,280 +374,3 @@
}
-##### plot
-plotWfm <- function(fit,inf,annoFile,minPos,maxPos,trackFeature="exon",overlayFeature=c("gene","transposable_element_gene"),two.strand=TRUE,plotData=TRUE,plotMean=TRUE,tracks=0)
-{
- if (missing(annoFile)) {stop("Annotation File is missing!!")}
- Gloc <- getProbePosition(fit)
- if (missing(minPos)) {minPos<-min(Gloc)}
- if (missing(maxPos)) {maxPos<-max(Gloc)}
- chromosome <- getChromosome(fit)
- strand <- getStrand(fit)
- selID <- (1:length(Gloc))[Gloc>minPos & Gloc<maxPos]
- sta <- min(selID)
- end <- max(selID)
- minBase <- Gloc[sta]
- maxBase <- Gloc[end]
- trackCount <- 1
- trackInfo <- list()
- overlayInfo <- list()
- if (plotData==TRUE)
- {
- Y <- getDataOrigSpace(fit)
- replcs <- as.numeric(table(getPhenoInfo(fit)$group))
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(t(Y[,sta:end])),probeStart=Gloc[sta:end],dp=DisplayPars(color=rep(1:length(replcs),replcs),ylim=range(Y[,sta:end]),pointSize=.3,pch=sequence(replcs)))
- names(trackInfo)[trackCount] <- "Data"
- trackCount <- trackCount + 1
- }
- if (two.strand==TRUE)
- {
- trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="forward",feature=trackFeature,dp=NULL)
- names(trackInfo)[trackCount] <- "F"
- overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="forward",region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
- trackCount <- trackCount + 1
- trackInfo[[trackCount]] <- makeGenomeAxis(add53 = TRUE,add35 = TRUE)
- trackCount <- trackCount + 1
- trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="reverse",feature=trackFeature)
- names(trackInfo)[trackCount] <- "R"
- overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand="reverse",region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
- trackCount <- trackCount + 1
- } else
- {
- trackInfo[[trackCount]] <- makeNewAnnotationTrack(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand=strand,feature=trackFeature)
- if (strand=="forward")
- {
- names(trackInfo)[trackCount] <- "F"
- }
- if (strand=="reverse")
- {
- names(trackInfo)[trackCount] <- "R"
- }
- overlayInfo[[trackCount]] <- makeNewAnnotationTextOverlay(annoFile=annoFile,chromosome=chromosome,minBase=minBase,maxBase=maxBase,strand=strand,region=c(trackCount,trackCount),feature=overlayFeature,y=0.5)
- trackCount <- trackCount + 1
- gAxis <- makeGenomeAxis(add53 = TRUE,add35 = TRUE)
- trackCount <- trackCount + 1
- }
- effects <- getEff(inf)
- regions <- getRegions(inf)
- noGroups <- length(table(getPhenoInfo(fit)$group))
- if (inherits(inf,"WfmInfMeans")) {
- plotMean <- FALSE
- }
- if (plotMean==TRUE)
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[1,sta:end])+c(-0.4,0.4),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- "Mean"
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[1]]),end(regions[[1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- trackCount <- trackCount + 1
- }
-# if (getWfmFitMethod(object)=="twoGroup" | getWfmFitMethod(object)=="circadian")
- if ((inherits(fit,"WfmFitFactor") & noGroups==2) | inherits(fit,"WfmFitCircadian"))
- {
- if (tracks==0)
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[2,sta:end])[1]),max(1.3,range(effects[2,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- #if (getWfmFitMethod(object)=="twoGroup")
- if (inherits(inf,"WfmInfCompare"))
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[2,sta:end])[1]),max(1.3,range(effects[2,sta:end])[2])+c(-0.2,0.2)),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- "FC"
- } else
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2)),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2))[1]),max(1.2,range(sqrt(effects[2,sta:end]^2+effects[3,sta:end]^2))))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- "Ampl"
- }
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[2]]),end(regions[[2]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
- }
- }
-# if (getWfmFitMethod(object)=="compareGroupsTime" | getWfmFitMethod(object)=="compareGroupsFactor")
- else if (inherits(inf,"WfmInfCompare"))
- {
- if (length(tracks)==1 & tracks[1]==0)
- {
-
- effectsToPlot <- rep(0,noGroups)
- effectId <- c(1,3,6,10,15)
- effectNames <- c("2-1","3-2","4-3","5-4","6-5")
- effectNo <- 1
- while (effectNo<length(effectsToPlot))
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[effectId[effectNo]+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[effectId[effectNo]+1,sta:end])[1]),max(1.3,range(effects[effectId[effectNo]+1,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- effectNames[effectNo]
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[effectId[effectNo]+1]]),end(regions[[effectId[effectNo]+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- effectNo <- effectNo + 1
- trackCount <- trackCount + 1
- }
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[effectId[length(effectsToPlot)-2]+2,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[effectId[length(effectsToPlot)-2]+2,sta:end])[1]),max(1.3,range(effects[effectId[length(effectsToPlot)-2]+2,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- "Last-First"
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[effectId[length(effectsToPlot)-2]+2]]),end(regions[[effectId[length(effectsToPlot)-2]+2]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
-
- }
- if (length(tracks)>1 | tracks[1]!=0)
- {
- if (length(tracks)>8)
- {
- stop("Too many tracks specified")
- }
- groupNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
- #groupNames <- sapply(8:13,function(x) paste("D",x,sep=""))
- firstId <- rep(2:noGroups,1:(noGroups-1))
- lastId <- sequence(1:(noGroups-1))
- effectNames <- sapply(1:(noGroups*(noGroups-1)/2),function(x) paste(groupNames[firstId[x]],"-",groupNames[lastId[x]],sep=""))
- for (i in tracks)
- {
- #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i+1,sta:end])[1]),max(1.3,range(effects[i+1,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[,sta:end])+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- effectNames[i]
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i+1]]),end(regions[[i+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- trackCount <- trackCount + 1
- }
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
- }
-
- }
-# if (getWfmFitMethod(object)=="meansByGroupTime" | getWfmFitMethod(object)=="meansByGroupFactor")
- else if (inherits(inf,"WfmInfMeans"))
- {
- if (length(tracks)==1 & tracks[1]==0)
- {
- effectNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
- for (i in 1:noGroups)
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i,sta:end])[1]),max(1.3,range(effects[i,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- effectNames[i]
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i]]),end(regions[[i]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- trackCount <- trackCount + 1
- }
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
- }
- if (length(tracks)>1 | tracks[1]!=0)
- {
- if (length(tracks)>8)
- {
- stop("Too many tracks specified")
- }
- #effectNames <- sapply(1:noGroups,function(x) paste("Gr",x,sep=""))
- effectNames <- paste("day",8:13,sep="")
- for (i in tracks)
- {
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=c(min(-1.3,range(effects[i,sta:end])[1]),max(1.3,range(effects[i,sta:end])[2]))+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[,sta:end])+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- effectNames[i]
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i]]),end(regions[[i]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- trackCount <- trackCount + 1
- }
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
- }
- }
-# if (getWfmFitMethod(object)=="effectsTime")
- else if (inherits(fit,"WfmFitTime") & inherits(inf,"WfmInfEffects"))
- {
- fct <- 0.2390457
- if (tracks==0 | (length(tracks)==2 & tracks[1]==1 & tracks[2]==2) | tracks==1 | tracks==2)
- {
- if (tracks==0)
- {
- tracks <- c(1,2)
- }
- effectNames <- c("Linear","Quadratic")
- for (i in tracks)
- {
- #trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[i+1,sta:end])+c(-0.5,0.5),pointSize=.3,pch=1,lwd=1,type="line"))
- trackInfo[[trackCount]] <- makeGenericArray(intensity=as.matrix(effects[i+1,sta:end]*fct),probeStart=Gloc[sta:end],dp=DisplayPars(color="black",ylim=range(effects[i+1,sta:end]*fct)+c(-0.2,0.2),pointSize=.3,pch=1,lwd=1,type="line"))
- names(trackInfo)[trackCount] <- effectNames[i]
- overlayInfo[[trackCount]] <- makeNewTranscriptRectangleOverlay(sigRegions=as.matrix(data.frame(start(regions[[i+1]]),end(regions[[i+1]]))),location=Gloc,start=sta,end=end,region=c(trackCount,trackCount),dp=DisplayPars(color="darkgrey",alpha=.1))
- trackCount <- trackCount + 1
- }
- hlp <- which(!unlist(lapply(overlayInfo,is.null)))
- if (two.strand==TRUE)
- {
- hlpAnno <- hlp[1:2]
- } else
- {
- hlpAnno <- hlp[1]
- }
- hlpAnnoIndex <- unlist(lapply(hlpAnno,function(x) length(overlayInfo[[x]]@xpos)>0))
- hlpEff <- hlp[!(hlp%in%hlpAnno)]
- hlpEffIndex <- unlist(lapply(hlpEff,function(x) length(overlayInfo[[x]]@start)>0))
- hlpIndex <- c(hlpAnnoIndex,hlpEffIndex)
- overlayInfoCorr <- lapply(hlp,function(x) overlayInfo[[x]])
- gdPlot(trackInfo,minBase=minBase,maxBase=maxBase,overlay=overlayInfoCorr[hlpIndex])
- } else
- {
- stop("tracks argument has been misspecified")
- }
- }
- else if (inherits(inf,"WfmInfCustom")) {
- stop("Custom Inference plot not implemented!")
- }
- else {
- stop("Unknown Design")
- }
-}
\ No newline at end of file
Deleted: pkg/inst/doc/Makefile
===================================================================
--- pkg/inst/doc/Makefile 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/inst/doc/Makefile 2012-05-15 09:41:23 UTC (rev 38)
@@ -1,10 +0,0 @@
-all: waveTiling clean
-
-waveTiling: waveTiling-vignette.tex
-cp -p ../inst/scripts/waveTiling-vignette.pdf .
-
-clean:
- $(RM) -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
- $(RM) -f Rplots.pdf waveTiling-*
-
-
Deleted: pkg/inst/doc/waveTiling-vignette.Rnw
===================================================================
--- pkg/inst/doc/waveTiling-vignette.Rnw 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/inst/doc/waveTiling-vignette.Rnw 2012-05-15 09:41:23 UTC (rev 38)
@@ -1,16 +0,0 @@
-%\VignetteIndexEntry{The waveTiling package}
-%\VignetteDepends{waveTiling}
-%\VignettePackage{waveTiling}
-
-% ---- This is just a stub. -----
-% The real .Rnw source for this vignette is in inst/scripts/waveTiling.Rnw
-% It cannot be put here (inst/doc/) since it takes too much time and memory to run.
-% So it needs to be run manually, and the resulting PDF is distributed as part
-% of the source package. See the 'Makefile' in this directory, which will
-% copy the PDF from ../scripts to here.
-
-\documentclass[10pt]{article}
-\begin{document}
-nonlinear
-\end{document}
-
Deleted: pkg/inst/doc/waveTiling-vignette.pdf
===================================================================
(Binary files differ)
Modified: pkg/man/GenomeInfo-class.Rd
===================================================================
--- pkg/man/GenomeInfo-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/GenomeInfo-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,6 +2,7 @@
\Rdversion{1.1}
\docType{class}
\alias{GenomeInfo-class}
+\alias{GenomeInfo}
\alias{initialize,GenomeInfo-method}
\alias{show,GenomeInfo-method}
Modified: pkg/man/MapFilterProbe-class.Rd
===================================================================
--- pkg/man/MapFilterProbe-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/MapFilterProbe-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,10 +2,15 @@
\Rdversion{1.1}
\docType{class}
\alias{MapFilterProbe-class}
+\alias{MapFilterProbe}
\alias{getChromosome,MapFilterProbe-method}
+\alias{getChromosome}
\alias{getFilteredIndices,MapFilterProbe-method}
+\alias{getFilteredIndices}
\alias{getPosition,MapFilterProbe-method}
+\alias{getPosition}
\alias{getStrand,MapFilterProbe-method}
+\alias{getStrand}
\alias{initialize,MapFilterProbe-method}
\alias{selectProbesFromFilterOverlap,MapFilterProbe-method}
\alias{show,MapFilterProbe-method}
@@ -14,6 +19,20 @@
\description{class to store probe information after remapping and/or filtering of probes.}
+\usage{
+
+## Accessors
+
+getChromosome(object)
+getFilteredIndices(object)
+getPosition(object)
+getStrand(object)
+}
+
+\arguments{
+ \item{object}{An instance of \code{MapFilterProbe}-class.}
+}
+
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("mapFilterProbe", filteredIndices, chromosome, position, strand)}.}
@@ -25,6 +44,7 @@
\item{\code{strand}:}{Object of class \code{"vector"} ~~ }
}
}
+
\section{Methods}{
\describe{
\item{getChromosome}{\code{signature(object = "MapFilterProbe")}: ... }
@@ -37,10 +57,37 @@
}
}
+\section{Accessors}{
+ In the following code snippets, \code{x} is a MapFilterProbe object.
+ \describe{
+ \item{}{
+ \code{getChromosome(x): Extract the chromosome identifiers.}
+ }
+ \item{}{
+ \code{getFilteredIndices(x): Extract the filtered probe indices.}
+ }
+ \item{}{
+ \code{getPosition(x): Extract the genomic position of the filtered probes.}
+ }
+ \item{}{
+ \code{getStrand(x): Extract the strand orientation info for the filtered probes.}
+ }
+ }
+}
+
+
\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
\examples{
-showClass("MapFilterProbe")
+ showClass("MapFilterProbe")
+ \dontrun{
+ library(waveTilingData)
+ data(leafdevMapAndFilterTAIR9)
+ tt1 <- getChromsome(leafdevMapAndFilterTAIR9)
+ tt2 <- getFilteredIndices(leafdevMapAndFilterTAIR9)
+ tt3 <- getPosition(leafdevMapAndFilterTAIR9)
+ tt4 <- getStrand(leafdevMapAndFilterTAIR9)
+ }
}
\keyword{classes}
Modified: pkg/man/WaveTilingFeatureSet-class.Rd
===================================================================
--- pkg/man/WaveTilingFeatureSet-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WaveTilingFeatureSet-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,14 +2,18 @@
\Rdversion{1.1}
\docType{class}
\alias{WaveTilingFeatureSet-class}
+\alias{WaveTilingFeatureSet}
\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}
\alias{getGroupNames,WaveTilingFeatureSet-method}
+\alias{getNoGroups}
\alias{getNoGroups,WaveTilingFeatureSet-method}
+\alias{getReplics}
\alias{getReplics,WaveTilingFeatureSet-method}
\alias{selectProbesFromTilingFeatureSet,WaveTilingFeatureSet-method}
\alias{wfm.fit,WaveTilingFeatureSet-method}
@@ -18,6 +22,19 @@
\description{Class to store expression and phenotypic data from a tiling array experiment, used as input for the wavelet-based transcriptome analysis.}
+\usage{
+
+## Accessors
+
+getGroupNames(object)
+getNoGroups(object)
+getReplics(object)
+}
+
+\arguments{
+ \item{object}{An instance of \code{WaveTilingFeatureSet}-class.}
+}
+
\section{Objects from the Class}{Objects can be created by calls of the form \code{new("WaveTilingFeatureSet")}.}
\section{Slots}{
@@ -56,10 +73,34 @@
}
}
+\section{Accessors}{
+ In the following code snippets, \code{x} is a WaveTilingFeatureSet object.
+ \describe{
+ \item{}{
+ \code{getGroupNames(x): Extract the group or sample names in the tiling array experiment.}
+ }
+ \item{}{
+ \code{getNoGroups(x): Extract the number of groups or samples in the tiling array experiment.}
+ }
+ \item{}{
+ \code{getReplics(x): Extract the number of replicates in the tiling array experiment.}
+ }
+ }
+}
+
\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
\examples{
-showClass("WaveTilingFeatureSet")
+ showClass("WaveTilingFeatureSet")
+ \dontrun{
+ data(leafdev)
+ leafdev <- as(leafdev,"WaveTilingFeatureSet")
+ leafdev <- addPheno(leafdev,noGroups=6,groupNames=c("day8","day9","day10","day11","day12","day13"),replics=rep(3,6))
+ tt1 <- getGroupNames(leafdev)
+ tt2 <- getNoGroups(leafdev)
+ tt3 <- getReplics(leafdev)
+ }
+
}
\keyword{classes}
Modified: pkg/man/WfmFit-class.Rd
===================================================================
--- pkg/man/WfmFit-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WfmFit-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,34 +2,84 @@
\Rdversion{1.1}
\docType{class}
\alias{WfmFit-class}
+\alias{WfmFit}
\alias{show,WfmFit-method}
\alias{initialize,WfmFit-method}
+\alias{getProbePosition}
\alias{getProbePosition,WfmFit-method}
+\alias{getNoProbes}
\alias{getNoProbes,WfmFit-method}
+\alias{getBetaWav}
\alias{getBetaWav,WfmFit-method}
+\alias{getVarBetaWav}
\alias{getVarBetaWav,WfmFit-method}
+\alias{getSmoothPar}
\alias{getSmoothPar,WfmFit-method}
+\alias{getVarEps}
\alias{getVarEps,WfmFit-method}
+\alias{getGenomeInfo}
\alias{getGenomeInfo,WfmFit-method}
\alias{getChromosome,WfmFit-method}
\alias{getStrand,WfmFit-method}
+\alias{getMinPos}
\alias{getMinPos,WfmFit-method}
+\alias{getMaxPos}
\alias{getMaxPos,WfmFit-method}
+\alias{getNoLevels}
\alias{getNoLevels,WfmFit-method}
+\alias{getDesignMatrix}
\alias{getDesignMatrix,WfmFit-method}
+\alias{getPhenoInfo}
\alias{getPhenoInfo,WfmFit-method}
+\alias{getDataOrigSpace}
\alias{getDataOrigSpace,WfmFit-method}
+\alias{getDataWaveletSpace}
\alias{getDataWaveletSpace,WfmFit-method}
+\alias{getWaveletFilter}
\alias{getWaveletFilter,WfmFit-method}
+\alias{getKj}
\alias{getKj,WfmFit-method}
+\alias{getPrior}
\alias{getPrior,WfmFit-method}
+\alias{getF}
\alias{getF,WfmFit-method}
+\alias{getVarF}
\alias{getVarF,WfmFit-method}
\alias{wfm.inference,WfmFit-method}
\title{Class "WfmFit"}
+
\description{class to store model fits in the wavelet-based transcriptome analysis.}
+\usage{
+
+## Accessors
+
+getProbePosition(object)
+getNoProbes(object)
+getBetaWav(object)
+getVarBetaWav(object)
+getSmoothPar(object)
+getVarEps(object)
+getGenomeInfo(object)
+getMinPos(object)
+getMaxPos(object)
+getNoLevels(object)
+getDesignMatrix(object)
+getPhenoInfo(object)
+getDataOrigSpace(object)
+getDataWaveletSpace(object)
+getWaveletFilter(object)
+getKj(object)
+getPrior(object)
+getF(object)
+getVarF(object)
+}
+
+\arguments{
+ \item{object}{An instance of \code{WfmFit}-class.}
+}
+
\section{Objects from the Class}{Objects can be created by calls of the form \code{new("WfmFit", betaWav, varbetaWav, smoothPar, varEps, dataOrigSpace, dataWaveletSpace, design.matrix, phenoData, genome.info, n.levels, probePosition, wave.filt, Kj, prior, F, varF, P, Z, noGroups, replics)}.}
\section{Slots}{
@@ -87,10 +137,106 @@
}
}
+\section{Accessors}{
+ In the following code snippets, \code{x} is a WfmFit object.
+ \describe{
+ \item{}{
+ \code{getBetaWav(x): Extract the fitted effect functions in the wavelet space.}
+ }
+ \item{}{
+ \code{getChromsome(x): Extract the chromosome identifiers.}
+ }
+ \item{}{
+ \code{getDataOrigSpace(x): Extract the raw expression data in the original data space.}
+ }
+ \item{}{
+ \code{getDataWaveletSpace(x): Extract the raw data in the wavelet space, i.e. the wavelet coefficients.}
+ }
+ \item{}{
+ \code{getDesignMatrix(x): Extract the design matrix used in the wavelet-based analysis.}
+ }
+ \item{}{
+ \code{getF(x): Extract the fitted functional effects in the original data space.}
+ }
+ \item{}{
+ \code{getGenomeInfo(x): Extract the genomic information.}
+ }
+ \item{}{
+ \code{getKj(x): Extract the number of wavelet coefficients estimated per wavelet level.}
+ }
+ \item{}{
+ \code{getMaxPos(x): Extract the maximum genomic probe position.}
+ }
+ \item{}{
+ \code{getMinPos(x): Extract the minimum genomic probe position.}
+ }
+ \item{}{
+ \code{getNoLevels(x): Extract the number of levels in in the wavelet decomposition when fitting the wavelet-based functional model.}
+ }
+ \item{}{
+ \code{getNoProbes(x): Extract the number of probes.}
+ }
+ \item{}{
+ \code{getPhenoInfo(x): Extract the phenotypic information for the tiling array experiment.}
+ }
+ \item{}{
+ \code{getPrior(x): Extract the the type or distribution of the prior imposed on the functional effects in the wavelet space.}
+ }
+ \item{}{
+ \code{getProbePosition(x): Extract probe position.}
+ }
+ \item{}{
+ \code{getSmoothPar(x): Extract the estimated smoothing parameters that control the regularization of the effect functions in the wavelet space.}
+ }
+ \item{}{
+ \code{getStrand(x): Extract the strand orientation info.}
+ }
+ \item{}{
+ \code{getVarBetaWav(x): Extract the variance of the fitted effect functions in the wavelet space.}
+ }
+ \item{}{
+ \code{getVarEps(x): Extract the estimated residual variance in the wavelet space. One variance parameter is estimated per wavelet level.}
+ }
+ \item{}{
+ \code{getVarF(x): Extract the variance of the fitted functional effects in the original data space.}
+ }
+ \item{}{
+ \code{getWaveletFilter(x): Extract the wavelet filter used to transform the data from the original space to the wavelet space.}
+ }
+ }
+}
+
+
\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
\examples{
-showClass("WfmFit")
+ showClass("WfmFit")
+
+ \dontrun{
+ library(waveTilingData)
+ data(leafdevFit)
+ tt1 <- getBetaWav(leafdevFit)
+ tt2 <- getChromosome(leafdevFit)
+ tt3 <- getDataOrigSpace(leafdevFit)
+ tt4 <- getDataWaveletSpace(leafdevFit)
+ tt5 <- getDesignMatrix(leafdevFit)
+ tt6 <- getF(leafdevFit)
+ tt7 <- getGenomeInfo(leafdevFit)
+ tt8 <- getKj(leafdevFit)
+ tt9 <- getMaxPos(leafdevFit)
+ tt10 <- getMinPos(leafdevFit)
+ tt11 <- getNoLevels(leafdevFit)
+ tt12 <- getNoProbes(leafdevFit)
+ tt13 <- getPhenoInfo(leafdevFit)
+ tt14 <- getPrior(leafdevFit)
+ tt15 <- getProbePosition(leafdevFit)
+ tt16 <- getSmoothPar(leafdevFit)
+ tt17 <- getStrand(leafdevFit)
+ tt18 <- getVarBetaWav(leafdevFit)
+ tt19 <- getVarEps(leafdevFit)
+ tt20 <- getVarF(leafdevFit)
+ tt21 <- getWaveletFilter(leafdevFit)
+ }
}
\keyword{classes}
Modified: pkg/man/WfmFitCircadian-class.Rd
===================================================================
--- pkg/man/WfmFitCircadian-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WfmFitCircadian-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,6 +2,7 @@
\Rdversion{1.1}
\docType{class}
\alias{WfmFitCircadian-class}
+\alias{WfmFitCircadian}
\alias{show,WfmFitCircadian-method}
\alias{initialize,WfmFitCircadian-method}
Modified: pkg/man/WfmFitCustom-class.Rd
===================================================================
--- pkg/man/WfmFitCustom-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WfmFitCustom-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,6 +2,7 @@
\Rdversion{1.1}
\docType{class}
\alias{WfmFitCustom-class}
+\alias{WfmFitCustom}
\alias{show,WfmFitCustom-method}
\alias{initialize,WfmFitCustom-method}
Modified: pkg/man/WfmFitFactor-class.Rd
===================================================================
--- pkg/man/WfmFitFactor-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WfmFitFactor-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,6 +2,7 @@
\Rdversion{1.1}
\docType{class}
\alias{WfmFitFactor-class}
+\alias{WfmFitFactor}
\alias{show,WfmFitFactor-method}
\alias{initialize,WfmFitFactor-method}
Modified: pkg/man/WfmFitTime-class.Rd
===================================================================
--- pkg/man/WfmFitTime-class.Rd 2012-04-24 06:36:45 UTC (rev 37)
+++ pkg/man/WfmFitTime-class.Rd 2012-05-15 09:41:23 UTC (rev 38)
@@ -2,6 +2,7 @@
\Rdversion{1.1}
\docType{class}
\alias{WfmFitTime-class}
+\alias{WfmFitTime}
\alias{show,WfmFitTime-method}
\alias{initialize,WfmFitTime-method}
Modified: pkg/man/WfmInf-class.Rd
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/wavetiling -r 38
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