[Wavetiling-commits] r35 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 18 11:38:52 CEST 2012
Author: kdbeuf
Date: 2012-04-18 11:38:52 +0200 (Wed, 18 Apr 2012)
New Revision: 35
Modified:
pkg/DESCRIPTION
pkg/R/helperFunctions.R
pkg/R/methods-WaveTilingFeatureSet.R
pkg/R/methods-WfmFit.R
pkg/R/methods-WfmInf.R
pkg/man/plotWfm.Rd
Log:
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/DESCRIPTION 2012-04-18 09:38:52 UTC (rev 35)
@@ -1,5 +1,5 @@
Package: waveTiling
-Version: 0.1.1
+Version: 0.1.35
Date: 2012-02-16
License: GPL (>=2)
Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
Modified: pkg/R/helperFunctions.R
===================================================================
--- pkg/R/helperFunctions.R 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/R/helperFunctions.R 2012-04-18 09:38:52 UTC (rev 35)
@@ -207,7 +207,7 @@
}
} else
{
- if (trace==TRUE) cat("Gauss Seidel algorithm...")
+ if (trace==TRUE) message("Gauss Seidel algorithm...")
for (j in 1:max.it)
{
crit0 <- crit1
@@ -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) cat("\n iteration", j,"of",max.it)
+ if (trace==TRUE) message("\n iteration", j,"of",max.it)
if ((abs((crit0-crit1)/crit0))<tol)
{
- if (trace==TRUE) cat("\n Gauss Seidel algorithm converged \n")
+ if (trace==TRUE) message("\n Gauss Seidel algorithm converged \n")
break
}
}
- if ((abs(crit0-crit1)/crit0)>tol) cat("\n Warning: The maximum number of iterations reached without convergence\n")
+ if ((abs(crit0-crit1)/crit0)>tol) message("\n Warning: The maximum number of iterations reached without convergence\n")
}
if (!saveall)
{
Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/R/methods-WaveTilingFeatureSet.R 2012-04-18 09:38:52 UTC (rev 35)
@@ -96,10 +96,10 @@
trBand <- max(setTrustBand,minTrustBand)
if ((strand=="forward") | (strand=="both"))
{
- cat("begin remapping forward strand...\n")
- cat("extract probe sequences\n")
+ message("begin remapping forward strand...\n")
+ message("extract probe sequences\n")
pmSeqDict <- PDict(dataPMSeq,tb.start=1,tb.end=trBand)
- cat("match probe sequences to DNA sequence\n")
+ message("match probe sequences to DNA sequence\n")
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))
- cat("remapping forward strand done\n")
+ message("remapping forward strand done\n")
}
if ((strand=="reverse") | (strand=="both"))
{
- cat("begin remapping reverse strand...\n")
+ message("begin remapping reverse strand...\n")
## Fix me: sometimes reverseComplement/sometimes not?
dataPMSeqRevComp <- reverseComplement(pmSequence(object))
#dataPMSeqRevComp <- pmSequence(object)
@@ -140,7 +140,7 @@
}
names(chrSeqList) <- seqnames(BSgenomeObject)[chrId]
}
- cat("match probe sequences to DNA sequence\n")
+ message("match probe sequences to DNA sequence\n")
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))
- cat("remapping reverse strand done\n")
+ message("remapping reverse strand done\n")
}
}
else
@@ -184,7 +184,7 @@
pmMmOverlap <- NULL
if (strand=="both")
{
- cat("filter overlaps forward-reverse strand\n")
+ message("filter overlaps forward-reverse strand\n")
## 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)
{
- cat("filter overlaps PM-MM\n")
+ message("filter overlaps PM-MM\n")
if (strand=="forward")
{
dataMMSeq <- pm2mm(dataPMSeq)
Modified: pkg/R/methods-WfmFit.R
===================================================================
--- pkg/R/methods-WfmFit.R 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/R/methods-WfmFit.R 2012-04-18 09:38:52 UTC (rev 35)
@@ -363,7 +363,7 @@
effCosSampl <- rnorm(P,eff[3,],sqrt(varEff[3,]))
amplSampl <- sqrt(effSinSampl^2 + effCosSampl^2)
FDR[2,] <- FDR[2,] + (amplSampl < delta[2])
- if (k%%100==0) cat(k," ")
+ if (k%%100==0) message(k," ")
# calculate CIs: to do
}
FDR[2,] <- FDR[2,]/nsim
Modified: pkg/R/methods-WfmInf.R
===================================================================
--- pkg/R/methods-WfmInf.R 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/R/methods-WfmInf.R 2012-04-18 09:38:52 UTC (rev 35)
@@ -75,7 +75,7 @@
annoChrGeneGR <- annoChrGR[geneId]
#annoChrGeneStrandGR <- annoChrGeneGR[strand(annoChrGeneGR)==strandAlt]
#annoChrGeneStrandOppGR <- annoChrGeneGR[strand(annoChrGeneGR)==strandOpp]
- cat("find overlaps with detected regions...\n")
+ message("find overlaps with detected regions...\n")
nList <- length(regions)
annoOver <- GRangesList()
for (j in 1:nList)
@@ -115,13 +115,13 @@
strandAlt <- "-"
strandOpp <- "+"
}
- cat("get annotated regions...\n")
+ message("get annotated regions...\n")
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)
- cat("find overlaps with detected regions...\n")
+ message("find overlaps with detected regions...\n")
for (j in 1:nList)
{
regGlocIR <- regions[[j]]
Modified: pkg/man/plotWfm.Rd
===================================================================
--- pkg/man/plotWfm.Rd 2012-04-18 09:01:39 UTC (rev 34)
+++ pkg/man/plotWfm.Rd 2012-04-18 09:38:52 UTC (rev 35)
@@ -26,6 +26,12 @@
\value{nothing returned}
+\references{
+[1] Durinck S, Bullard J, Spellman PT, Dudoit S: GenomeGraphs: integrated genomic data visualization with R.
+BMC Bioinformatics 2009, 10:Article 2.
+}
+
+
\author{Kristof De Beuf <kristof.debeuf at ugent.be>}
\examples{
More information about the Wavetiling-commits
mailing list