[Wavetiling-commits] r9 - in pkg: . R man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 13 13:18:36 CET 2011 

Author: kdbeuf
Date: 2011-12-13 13:18:35 +0100 (Tue, 13 Dec 2011)
New Revision: 9

Modified:
   pkg/R/allClasses.R
   pkg/R/initialize-methods.R
   pkg/TODO
   pkg/man/addPheno.Rd
   pkg/man/bgCorrQn.Rd
   pkg/man/filterOverlap.Rd
   pkg/man/getGroupNames.Rd
   pkg/man/getNoGroups.Rd
   pkg/man/getReplics.Rd
   pkg/man/makeDesign.Rd
   pkg/man/selectProbesFromFilterOverlap.Rd
   pkg/man/selectProbesFromTilingFeatureSet.Rd
   pkg/man/wfm.analysis.Rd
Log:
WaveTilingFeatureSet


Modified: pkg/R/allClasses.R
===================================================================
--- pkg/R/allClasses.R	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/R/allClasses.R	2011-12-13 12:18:35 UTC (rev 9)
@@ -7,6 +7,6 @@
 #Wfm
 setClass("Wfm",representation(betaMAP="matrix",varbetaMAP="matrix",smoothPar="matrix",varEps="numeric",dataOrigSpace="matrix",dataWaveletSpace="matrix",design="matrix",phenoData="data.frame",method="character",genome.info="genomeInfo",n.levels="numeric",probePosition="vector",wave.filt="character",Kj="numeric",prior="character",alpha="numeric",delta="numeric",two.sided="numeric",rescale="matrix",sigProbes="list",regions="list",GlocRegions="list",FDR="matrix",CI="array",F="matrix",varF="matrix",eff="matrix",varEff="matrix"))
 
-#waveTilingFeatureSet
-setClass("waveTilingFeatureSet",contains="TilingFeatureSet")
+#WaveTilingFeatureSet
+setClass("WaveTilingFeatureSet",contains="TilingFeatureSet")
 

Modified: pkg/R/initialize-methods.R
===================================================================
--- pkg/R/initialize-methods.R	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/R/initialize-methods.R	2011-12-13 12:18:35 UTC (rev 9)
@@ -53,79 +53,10 @@
 	return(.Object)	
 })
 
-## remark: found this also as constructors for "NChannelSet","FeatureSet" and "TilingFeatureSet" (selectMethod("initialize","TilingFeatureSet"))
 #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, ...)
 	callNextMethod(.Object);
 }
 )
 
-# > structure(function (.Object, ...)
-# > {
-# >     # check if the first argument is an ExpressionSet
-# >     # if so: initialize the object with it and tells .local not to
-# >     # overwrite slots corresponding to missing arguments.
-# >     # otherwise: s
-# >     overwrite.missing<- TRUE
-# >     dotargs<- list(...)   
-# >     if( length(dotargs)>  1&&  is(dotargs[[1]], 'ExpressionSet') ){       
-# >         .Object<- dotargs[[1]]       
-# >         overwrite.missing<- FALSE
-# >         dotargs<- dotargs[-1]
-# >     }       
-# > 
-# >     # .local should initialize (i.e. overwrite) a slot of .Object with
-# > its prototype only if overwrite.missing=TRUE, or in any case with the
-# > corresponding non missing argument for this slot.
-# >      .local<- function (.Object, overwrite.missing=TRUE, assayData,
-# > phenoData, featureData,
-# >          exprs = new("matrix"), ...)
-# >      {                  if (overwrite.missing&&  missing(assayData)) {
-# >     # stuff ...
-# >     }
-# >     # other stuff ...
-# >      }
-# > 
-# >     # call .local with overwrite.missing as its first argument
-# >     do.call(.local, c(list(.Object, overwrite.missing), dotargs))
-# >     
-# > }
-
-# setMethod("initialize","waveTilingFeatureSet",function(.Object, ...)
-# {
-# 	Object <- callNextMethod(.Object, ...)
-# 	return(Object)
-# })

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/TODO	2011-12-13 12:18:35 UTC (rev 9)
@@ -1,6 +1,6 @@
 KDB:
-1) wfm.analysis,waveTilingFeatureSet-method: check calculation of confidence intervals
-2) wfm.analysis,waveTilingFeatureSet-method: check implementation of "two.sided" (adapt according to SAGMB paper)
+1) wfm.analysis,WaveTilingFeatureSet-method: check calculation of confidence intervals
+2) wfm.analysis,WaveTilingFeatureSet-method: check implementation of "two.sided" (adapt according to SAGMB paper)
 3) plotWfm,Wfm-method: introduce option to give groupnames to put on Y-axis of plot
 4) getNonAnnotatedRegions,Wfm-method: make function more generic wrt how the strands and features in the annotation file are defined
 5) getNonAnnotatedRegions,Wfm-method: include option to give max./mean expression / FC per region
@@ -8,6 +8,5 @@
 7) getSigGenes,Wfm-method: add option to include thresholds (density, outliers,...)
 8) getSigGenes,Wfm-method: add option to also detect regions that don't overlap but are in the neighbourhood of annotated regions
 9) getSigGenes,Wfm-method: add option to include mean / max expression / FC for each gene
-10) filterOverlap,waveTilingFeatureSet-method: check if this function makes use of all the TilingFeatureSet functionalities as constructed in the oligo-package (eg. pmChr, pmStrand...) remark: pmStrand does not seem to work properly
+10) filterOverlap,WaveTilingFeatureSet-method: check if this function makes use of all the TilingFeatureSet functionalities as constructed in the oligo-package (eg. pmChr, pmStrand...) remark: pmStrand does not seem to work properly
 
-PRIORITY: 11) solve trouble with initialize-method waveTilingFeatureSet

Modified: pkg/man/addPheno.Rd
===================================================================
--- pkg/man/addPheno.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/addPheno.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -2,7 +2,7 @@
 \alias{addPheno}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
-Add phenotypic info to TilingFeatureSet
+Add phenotypic info to WaveTilingFeatureSet
 }
 
 \description{
@@ -16,7 +16,7 @@
 
 \arguments{
   \item{object}{
-object of type waveTilingFeatureSet
+object of type WaveTilingFeatureSet
 }
   \item{noGroups}{
 Number of groups in the tiling array experiment
@@ -37,7 +37,7 @@
 }
 
 \value{
-object of class TilingFeatureSet annotated with the phenotypic data
+object of class WaveTilingFeatureSet annotated with the phenotypic data
 }
 
 \references{

Modified: pkg/man/bgCorrQn.Rd
===================================================================
--- pkg/man/bgCorrQn.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/bgCorrQn.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -13,7 +13,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
   \item{useMapFilter}{
 NULL or object of class mapFilterProbe indicating the probes to use for background correction and quantile normalization

Modified: pkg/man/filterOverlap.Rd
===================================================================
--- pkg/man/filterOverlap.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/filterOverlap.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -13,7 +13,7 @@
 
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
   \item{remap}{
 determines whether the tiling array probe sequences have to be remapped to a more recent reference DNA sequence

Modified: pkg/man/getGroupNames.Rd
===================================================================
--- pkg/man/getGroupNames.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/getGroupNames.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -14,7 +14,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
 
 }

Modified: pkg/man/getNoGroups.Rd
===================================================================
--- pkg/man/getNoGroups.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/getNoGroups.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -14,7 +14,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
 
 }

Modified: pkg/man/getReplics.Rd
===================================================================
--- pkg/man/getReplics.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/getReplics.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -15,7 +15,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
 
 }

Modified: pkg/man/makeDesign.Rd
===================================================================
--- pkg/man/makeDesign.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/makeDesign.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -15,7 +15,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
   \item{method}{
 Wfm method to use

Modified: pkg/man/selectProbesFromFilterOverlap.Rd
===================================================================
--- pkg/man/selectProbesFromFilterOverlap.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/selectProbesFromFilterOverlap.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -2,7 +2,7 @@
 \alias{selectProbesFromFilterOverlap}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
-select probes (from FIlterOverlap)
+select probes (from FilterOverlap)
 }
 
 \description{

Modified: pkg/man/selectProbesFromTilingFeatureSet.Rd
===================================================================
--- pkg/man/selectProbesFromTilingFeatureSet.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/selectProbesFromTilingFeatureSet.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -2,7 +2,7 @@
 \alias{selectProbesFromTilingFeatureSet}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
-select probes (from TilingFeatureSet)
+select probes (from WaveTilingFeatureSet)
 }
 
 \description{
@@ -15,7 +15,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
   \item{chromosome}{
 chromosome

Modified: pkg/man/wfm.analysis.Rd
===================================================================
--- pkg/man/wfm.analysis.Rd	2011-12-12 13:33:29 UTC (rev 8)
+++ pkg/man/wfm.analysis.Rd	2011-12-13 12:18:35 UTC (rev 9)
@@ -15,7 +15,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{object}{
-object of class waveTilingFeatureSet
+object of class WaveTilingFeatureSet
 }
   \item{filter.overlap}{
 mapFilterProbe object

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