synchronize with release version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@89984 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -1,21 +1,19 @@
-Package: ChIPQC
-Type: Package
-Title: Quality metrics for ChIPseq data
+Package: ChIPQC
+Type: Package
+Title: Quality metrics for ChIPseq data
 Version: 1.1.2
-Date: 2014-04-15
-Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
-Maintainer: Tom Carroll <[email protected]>, Rory Stark <[email protected]>
-Description: Quality metrics for ChIPseq data
-biocViews: Sequencing, ChIPSeq, QualityControl, ReportWriting
-License: GPL (>= 3)
-LazyLoad: yes
-Depends: R (>= 3.0.0), ggplot2, DiffBind
-Imports: methods, utils, grDevices, stats, BiocGenerics (>= 0.8.0), IRanges,
-        GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.11),
-        Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.1.9),
-        Biobase, chipseq (>= 1.12.0), BiocParallel,
-        gtools, reshape2, Nozzle.R1
-Suggests: BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene,
-          TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,
-          TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene 
-Collate: ChIPQCsample-class.R ChIPQCexperiment-class.R sampleQC.R ChIPQC_IF.R plots.r dbaplots.R utilities.R report.r 
+Date: 2014-05-06
+Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
+Maintainer: Tom Carroll <[email protected]>, Rory Stark <[email protected]>
+Description: Quality metrics for ChIPseq data
+biocViews: Sequencing, ChIPSeq, QualityControl, ReportWriting
+License: GPL (>= 3)
+LazyLoad: yes
+Depends: R (>= 3.0.0), ggplot2, DiffBind
+Imports: BiocGenerics (>= 0.8.0), Rsamtools (>= 1.14.2), GenomicRanges (>= 1.14.4),
+         chipseq (>= 1.12.0), GenomicAlignments (>= 0.99.2), 
+        gtools, BiocParallel, methods, IRanges, reshape2, Nozzle.R1, Biobase,grDevices, stats, utils
+Suggests: BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene,
+          TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,
+          TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene 
+Collate: ChIPQCsample-class.R ChIPQCexperiment-class.R sampleQC.R ChIPQC_IF.R plots.r dbaplots.R utilities.R report.r 

NAMESPACE

@@ -1,10 +1,8 @@
-import(methods)
+importClassesFrom(GenomicRanges, GRanges, Seqinfo)
 
 importClassesFrom(IRanges, DataFrame, IRanges, Rle)
 
-import(GenomeInfoDb)
-
-importClassesFrom(GenomicRanges, GRanges)
+importClassesFrom(methods, character, list, numeric, oldClass)
 
 importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
                   colnames, duplicated, lapply, ncol, nrow, order,
@@ -15,13 +13,18 @@ importMethodsFrom(BiocParallel, bplapply)
 
 importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam)
 
+importMethodsFrom(GenomicRanges, seqlengths, "seqlengths<-",
+                  "seqlevels<-", seqnames)
+
 importMethodsFrom(IRanges, "%in%", as.list, as.matrix, "colnames<-",
                   countOverlaps, coverage, elementMetadata,
                   "elementMetadata<-", end, flank, gsub, mean, median,
                   merge, ranges, reduce, resize, "rownames<-",
                   runLength, runValue, sd, shiftApply, start, t,
                   viewMaxs, viewApply, Views, which, which.max, width)
 
+importMethodsFrom(methods, show)
+
 importMethodsFrom(Rsamtools, scanBamHeader, ScanBamParam)
 
 import(chipseq)
@@ -45,6 +48,8 @@ importFrom(gtools, running)
 
 importFrom(IRanges, "%over%", IRanges)
 
+importFrom(methods, as, new)
+
 importFrom(Nozzle.R1, addTo, asLink, asStrong, newCustomReport,
            newFigure, newList, newParagraph, newSection, newSubSection,
            newTable, writeReport)

R/ChIPQC_IF.R

@@ -1,4 +1,4 @@
-ChIPQCsample = function(reads, peaks, annotation="hg19", chromosomes=NULL, 
+ChIPQCsample = function(reads, peaks, annotation, chromosomes=NULL, 
                         mapQCth=15, blacklist, profileWin=400,fragmentLength=125,shifts=1:300,runCrossCor=FALSE) {
 
    if(missing(peaks)) peaks=NULL