[Wavetiling-commits] r36 - in pkg: . R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 24 07:26:12 CEST 2012
Author: kdbeuf
Date: 2012-04-24 07:26:12 +0200 (Tue, 24 Apr 2012)
New Revision: 36
Modified:
pkg/DESCRIPTION
pkg/R/helperFunctions.R
pkg/R/methods-WaveTilingFeatureSet.R
pkg/R/methods-WfmInf.R
Log:
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-18 09:38:52 UTC (rev 35)
+++ pkg/DESCRIPTION 2012-04-24 05:26:12 UTC (rev 36)
@@ -1,5 +1,5 @@
Package: waveTiling
-Version: 0.1.35
+Version: 0.1.36
Date: 2012-02-16
License: GPL (>=2)
Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
@@ -7,7 +7,7 @@
Maintainer: Kristof De Beuf <kristof.debeuf at UGent.be>
Depends: oligo, oligoClasses, Biobase, Biostrings
Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, GenomeGraphs, IRanges
-Suggests: BSgenome
+Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9
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/R/helperFunctions.R
===================================================================
--- pkg/R/helperFunctions.R 2012-04-18 09:38:52 UTC (rev 35)
+++ pkg/R/helperFunctions.R 2012-04-24 05:26:12 UTC (rev 36)
@@ -225,14 +225,14 @@
varEps[i] <- sum(D[,starts[i]:ends[i]]*VinvD)/(ends[i]-starts[i]+1)/N
}
crit1 <- -1/2*sum(log(t(X)%*%X%*%WaveFit$phi+rep(1,ncol(X))))-1/2*(log(varEps)%*%Kj)-N*K*log(2*pi)/2-N*K/2
- if (trace==TRUE) message("\n iteration", j,"of",max.it)
+ if (trace==TRUE) message("iteration ", j," of ",max.it)
if ((abs((crit0-crit1)/crit0))<tol)
{
- if (trace==TRUE) message("\n Gauss Seidel algorithm converged \n")
+ if (trace==TRUE) message("Gauss Seidel algorithm converged")
break
}
}
- if ((abs(crit0-crit1)/crit0)>tol) message("\n Warning: The maximum number of iterations reached without convergence\n")
+ if ((abs(crit0-crit1)/crit0)>tol) message("Warning: The maximum number of iterations reached without convergence")
}
if (!saveall)
{
Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R 2012-04-18 09:38:52 UTC (rev 35)
+++ pkg/R/methods-WaveTilingFeatureSet.R 2012-04-24 05:26:12 UTC (rev 36)
@@ -96,10 +96,10 @@
trBand <- max(setTrustBand,minTrustBand)
if ((strand=="forward") | (strand=="both"))
{
- message("begin remapping forward strand...\n")
- message("extract probe sequences\n")
+ message("begin remapping forward strand...")
+ message("extract probe sequences")
pmSeqDict <- PDict(dataPMSeq,tb.start=1,tb.end=trBand)
- message("match probe sequences to DNA sequence\n")
+ message("match probe sequences to DNA sequence")
chrSeqList <- list()
for (i in chrId)
{
@@ -121,11 +121,11 @@
posInit <- c()
posInit[mp[,1]] <- unlist(lapply(startPM,function(x) unlist(x[pmMatch])))
strandInit <- rep("forward",length(pmMatchIndex))
- message("remapping forward strand done\n")
+ message("remapping forward strand done")
}
if ((strand=="reverse") | (strand=="both"))
{
- message("begin remapping reverse strand...\n")
+ message("begin remapping reverse strand...")
## Fix me: sometimes reverseComplement/sometimes not?
dataPMSeqRevComp <- reverseComplement(pmSequence(object))
#dataPMSeqRevComp <- pmSequence(object)
@@ -140,7 +140,7 @@
}
names(chrSeqList) <- seqnames(BSgenomeObject)[chrId]
}
- message("match probe sequences to DNA sequence\n")
+ message("match probe sequences to DNA sequence")
startPMRevComp <- lapply(chrSeqList,function(x) startIndex(matchPDict(pmSeqDictRevComp,x)))
nposChrPMRevComp <- lapply(startPMRevComp,function(x) sapply(x,length))
pmMatchRevComp <- Reduce("+",nposChrPMRevComp)==1
@@ -156,7 +156,7 @@
posInitRevComp <- c()
posInitRevComp[mp[,1]] <- unlist(lapply(startPMRevComp,function(x) unlist(x[pmMatchRevComp])))
strandInitRevComp <- rep("reverse",length(pmMatchIndexRevComp))
- message("remapping reverse strand done\n")
+ message("remapping reverse strand done")
}
}
else
@@ -184,7 +184,7 @@
pmMmOverlap <- NULL
if (strand=="both")
{
- message("filter overlaps forward-reverse strand\n")
+ message("filter overlaps forward-reverse strand")
## should be done more efficiently with something in Biostrings... ("%in%" does not work)
dataPMSeqChar <- as.character(dataPMSeq)
dataPMSeqRevCompChar <- as.character(dataPMSeqRevComp)
@@ -193,7 +193,7 @@
}
if (MM)
{
- message("filter overlaps PM-MM\n")
+ message("filter overlaps PM-MM")
if (strand=="forward")
{
dataMMSeq <- pm2mm(dataPMSeq)
Modified: pkg/R/methods-WfmInf.R
===================================================================
--- pkg/R/methods-WfmInf.R 2012-04-18 09:38:52 UTC (rev 35)
+++ pkg/R/methods-WfmInf.R 2012-04-24 05:26:12 UTC (rev 36)
@@ -75,7 +75,7 @@
annoChrGeneGR <- annoChrGR[geneId]
#annoChrGeneStrandGR <- annoChrGeneGR[strand(annoChrGeneGR)==strandAlt]
#annoChrGeneStrandOppGR <- annoChrGeneGR[strand(annoChrGeneGR)==strandOpp]
- message("find overlaps with detected regions...\n")
+ message("find overlaps with detected regions...")
nList <- length(regions)
annoOver <- GRangesList()
for (j in 1:nList)
@@ -115,13 +115,13 @@
strandAlt <- "-"
strandOpp <- "+"
}
- message("get annotated regions...\n")
+ message("get annotated regions...")
annoExons <- annoFile[(annoFile$strand==strandAlt)&(annoFile$chromosome==chromosome)&((annoFile$feature=="exon")|(annoFile$feature=="pseudogenic_exon")),c("chromosome","strand","feature","ID","start","end")]
annoExonsOpp <- annoFile[(annoFile$strand==strandOpp)&(annoFile$chromosome==chromosome)&((annoFile$feature=="exon")|(annoFile$feature=="pseudogenic_exon")),c("chromosome","strand","feature","ID","start","end")]
regGlocNoAnnoSense <- list()
regGlocNoAnnoBoth <- list()
nList <- length(regions)
- message("find overlaps with detected regions...\n")
+ message("find overlaps with detected regions...")
for (j in 1:nList)
{
regGlocIR <- regions[[j]]
@@ -129,8 +129,8 @@
annoExonsOppIR <- IRanges(start=annoExonsOpp$start,end=annoExonsOpp$end)
overSense <- findOverlaps(regGlocIR,annoExonsIR)
overOpp <- findOverlaps(regGlocIR,annoExonsOppIR)
- noAnnoSenseId <- which(!(1:length(regGlocIR) %in% matchMatrix(overSense)[,1]))
- noAnnoOppId <- which(!(1:length(regGlocIR) %in% matchMatrix(overOpp)[,1]))
+ noAnnoSenseId <- which(!(1:length(regGlocIR) %in% as.matrix(overSense)[,1]))
+ noAnnoOppId <- which(!(1:length(regGlocIR) %in% as.matrix(overOpp)[,1]))
noAnnoBothId <- which((1:length(regGlocIR) %in% noAnnoSenseId) & (1:length(regGlocIR) %in% noAnnoOppId))
regGlocNoAnnoSense[[j]] <- regGlocIR[noAnnoSenseId]
regGlocNoAnnoBoth[[j]] <- regGlocIR[noAnnoBothId]
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