[Wavetiling-commits] r44 - in pkg: pd.atdschip.tiling pd.atdschip.tiling/man waveTiling/R

[noreply at r-forge.r-project.org]

Author: kdbeuf
Date: 2012-06-06 10:00:53 +0200 (Wed, 06 Jun 2012)
New Revision: 44

Modified:
   pkg/pd.atdschip.tiling/DESCRIPTION
   pkg/pd.atdschip.tiling/man/pkg.Rd
   pkg/waveTiling/R/helperFunctions.R
Log:


Modified: pkg/pd.atdschip.tiling/DESCRIPTION
===================================================================
--- pkg/pd.atdschip.tiling/DESCRIPTION	2012-06-04 12:28:07 UTC (rev 43)
+++ pkg/pd.atdschip.tiling/DESCRIPTION	2012-06-06 08:00:53 UTC (rev 44)
@@ -1,7 +1,7 @@
 Package: pd.atdschip.tiling
 Title: Platform Design Info for Affymetrix Atdschip_tiling
 Description: Platform Design Info for Affymetrix Atdschip_tiling
-Version: 0.0.1
+Version: 0.0.2
 Author: Kristof De Beuf
 Maintainer: Kristof De Beuf <kristof.debeuf at ugent.be>
 LazyLoad: yes

Modified: pkg/pd.atdschip.tiling/man/pkg.Rd
===================================================================
--- pkg/pd.atdschip.tiling/man/pkg.Rd	2012-06-04 12:28:07 UTC (rev 43)
+++ pkg/pd.atdschip.tiling/man/pkg.Rd	2012-06-06 08:00:53 UTC (rev 44)
@@ -9,6 +9,6 @@
   Annotation package for pd.atdschip.tiling built with pdInfoBuilder.
 }
 \details{
-  This package is to be used in conjunction with the oligo package.
+  This package is to be used in conjunction with the oligo package. It contains the platform design information for the AGRONOMICS1 tiling array for the plant species Arabidopsis thaliana (TAIR8 Genomebuild).
 }
 \keyword{package}

Modified: pkg/waveTiling/R/helperFunctions.R
===================================================================
--- pkg/waveTiling/R/helperFunctions.R	2012-06-04 12:28:07 UTC (rev 43)
+++ pkg/waveTiling/R/helperFunctions.R	2012-06-06 08:00:53 UTC (rev 44)
@@ -251,15 +251,6 @@
 }
 
 ## plot
-# annoFIle needs the following columns: "chromosome", "strand", "feature", "ID", "start", "end"
-# makeNewAnnotationTrack <- function(annoFile,chromosome,strand,minBase,maxBase,feature="exon",dp=NULL)
-# {
-# 	if (is.null(dp))
-# 	{
-# 		dp <- DisplayPars(exon="lightblue")
-# 	}
-# 	return(makeAnnotationTrack(regions=annoFile[(annoFile$chromosome==chromosome)&(annoFile$strand==strand)&(annoFile$start<maxBase)&(annoFile$end>minBase)&(annoFile$feature==feature),c("start","end","feature","group","ID")],dp=dp))
-# }
 
 makeNewAnnotationTrack <- function(biomartObj,chromosome,strand,minBase,maxBase,feature="exon",dp=NULL)
 {
@@ -270,21 +261,11 @@
 	exn <- exons(biomartObj)
 	exnId <- which((as.character(seqnames(exn))==as.character(chromosome)&(as.character(strand(exn))==strand)&(start(ranges(exn))>minBase)&(end(ranges(exn))<maxBase)))
 	exnSel <- exn[exnId]
-	regionObj <- data.frame(start=start(ranges(exnSel)),end=end(ranges(exnSel)),feature=feature,group=elementMetadata(exnSel)$exon_id,ID=rep(NA,length(exnSel)))
+	regionObj <- data.frame(start=start(ranges(exnSel)),end=end(ranges(exnSel)),feature=rep(feature,length(exnSel)),group=elementMetadata(exnSel)$exon_id,ID=rep(NA,length(exnSel)))
 	return(makeAnnotationTrack(regions=regionObj,dp=dp))
 }
 
 
-# makeNewAnnotationTextOverlay <- function(annoFile,chromosome,strand,minBase,maxBase,region,feature=c("gene","transposable_element_gene"),y=.5,dp=NULL)
-# {
-# 	if (is.null(dp))
-# 	{
-# 		dp=DisplayPars(cex=1)
-# 	}
-# 	annohlp <- annoFile[(annoFile$chromosome==chromosome)&(annoFile$strand==strand)&(annoFile$start<maxBase)&(annoFile$end>minBase)&(is.element(annoFile$feature,feature)),c("ID","start","end")]
-# 	return(makeTextOverlay(annohlp$ID,xpos=(annohlp$start+annohlp$end)/2,ypos=y,region=region,dp=dp))
-# }
-
 makeNewAnnotationTextOverlay <- function(biomartObj,chromosome,strand,minBase,maxBase,region,feature=c("gene","transposable_element_gene"),y=.5,dp=NULL)
 {
 	if (is.null(dp))