@@ -1,7 +1,7 @@

 Package: ChIPQC

 Type: Package

 Title: Quality metrics for ChIPseq data

-Version: 1.23.0

+Version: 1.23.1

 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.

@@ -24,11 +24,11 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

                   consensus=FALSE, bCount=FALSE, mapQCth=15, blacklist=NULL, 

                   profileWin=400,fragmentLength=125,shifts=1:300,...) {

-  if(class(experiment)=="character" || class(experiment)=="data.frame") {

+  if(sum(class(experiment)=="character") || sum(class(experiment)=="data.frame")) {

     experiment = dba(sampleSheet=experiment,bCorPlot=FALSE,peakCaller="bed")

   } 

-  if(class(experiment)!="DBA") {

+  if(!sum(class(experiment)=="DBA")) {

     stop("experiment must be either a samplesheet filename or a DBA (DiffBind) object.")

   }

@@ -70,7 +70,7 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

   if(!missing(annotation)) {

     if(!is.null(annotation) && missing(samples)) {

-      if(class(annotation)!="list") {

+      if(!sum(class(annotation)=="list")) {

         message('Compiling annotation...')

         annotation = getAnnotation(annotation,AllChr=chromosomes)

       }

@@ -80,7 +80,7 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

         blacklist = makeGRangesFromDataFrame(blacklist,ignore.strand=TRUE)

         message("Using default blacklist for hg19...")

       }

-    } else if(class(annotation)=="character") {

+    } else if(sum(class(annotation)=="character")) {

       annotation = list(version=annotation)

     } else {

       annotation = list(version="none")

@@ -129,10 +129,10 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

   setNull <- TRUE   

   peaks <- NA

-  if(class(consensus) == "GRanges") {

+  if(sum(class(consensus) == "GRanges")) {

     useConsensus <- TRUE

   } else {

-    if(class(consensus) == "logical") {

+    if(sum(class(consensus) == "logical")){

       if(consensus == TRUE) {

         useConsensus <- TRUE

       } else {

@@ -146,7 +146,7 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

   if(useConsensus == TRUE) {

     addcontrols  <- TRUE

     addconsensus <- TRUE

-    if(class(consensus) == "GRanges") {

+    if(sum(class(consensus) == "GRanges")) {

       peaks <- consensus

       setNull <- FALSE   

     } else {

@@ -219,7 +219,7 @@ ChIPQC = function(experiment, annotation, chromosomes, samples,

     errors = FALSE

     for(i in 1:length(samples)) {

       sample = samples[[i]]

-      if(class(sample) != "ChIPQCsample") {

+      if(!sum(class(sample) == "ChIPQCsample")) {

         message("Error in sample ",names(samples)[i],": ",sample[1])

         errors = TRUE

       }

@@ -25,7 +25,7 @@ makeSummarySection <- function(object){

   summarySection <- newSection( "QC Summary" );

   metrics <- QCmetrics(object)

-  if(class(object)=="ChIPQCexperiment"){

+  if(sum(class(object)=="ChIPQCexperiment")){

     metrics <- metrics[,!colnames(metrics) %in% c("ReadLenCC","RIBL","Map%","Filt%","ReadLen")]

     allMetadata <- QCmetadata(object)

     metadata <- allMetadata[,c("ID","Tissue","Factor","Condition","Replicate")]

@@ -136,7 +136,7 @@ makeMFDSection <- function(object,riblPlot,gfePlot){

                              "Total Dup%",

                              "Pass MapQ Filter%",

                              "Pass MapQ Filter and Dup%")

-  if(class(object)=="ChIPQCexperiment"){

+  if(sum(class(object)=="ChIPQCexperiment")){

     allMetadata <- QCmetadata(object)

     metadata <- allMetadata[,c("ID","Tissue","Factor","Condition","Replicate")]

@@ -54,11 +54,11 @@ sampleQC <- function(bamFile,bedFile=NULL,blklist=NULL,ChrOfInterest=NULL,GeneAn

   txdb <- NULL

   GeneAnnotationTotalSizes <- NULL

-  if(class(GeneAnnotation)!="list" & !is.null(GeneAnnotation)) {

+  if(!sum(class(GeneAnnotation)=="list") & !is.null(GeneAnnotation)) {

     GeneAnnotation = getAnnotation(GeneAnnotation,AllChr=names(ChrLengths))

   }

-  if(class(GeneAnnotation)=="list"){

+  if(sum(class(GeneAnnotation)=="list")){

     if(length(GeneAnnotation)>1) {

       GeneAnnotation <- GeneAnnotation[!names(GeneAnnotation) %in% "version"]

       GeneAnnotation <- lapply(GeneAnnotation,function(x)reduce(GetGRanges(x,names(ChrLengths))))

@@ -193,7 +193,7 @@ sampleQC <- function(bamFile,bedFile=NULL,blklist=NULL,ChrOfInterest=NULL,GeneAn

       }else{

         SSDBL <- NULL

       }

-      if(class(GeneAnnotation)=="list"){

+      if(sum(class(GeneAnnotation)=="list")){

         #GRangesOfInterestListGA <- GRangesList()

         noVersionGeneAnnotation <- GeneAnnotation[!names(GeneAnnotation)=="version"]

         GRangesOfInterestListGF <- GRangesList()

@@ -324,7 +324,7 @@ sampleQC <- function(bamFile,bedFile=NULL,blklist=NULL,ChrOfInterest=NULL,GeneAn

     SSDBLAv <- as.numeric(NA)     

   }   

-  if(class(GeneAnnotation)=="list" & !is.null(GFCountsMatrix)){

+  if(sum(class(GeneAnnotation)=="list") & !is.null(GFCountsMatrix)){

     #CountsInFeatures <-vector("list",length=ncol(GFCountsMatrix))

     CountsInFeatures <- as.list(apply(GFCountsMatrix,2,function(x)sum(x,na.rm=TRUE)))

     names(CountsInFeatures) <- colnames(GFCountsMatrix)

@@ -423,15 +423,15 @@ GetGRanges <- function(LoadFile,AllChr=NULL,ChrOfInterest=NULL,simple=FALSE,sepr

   #    require(Rsamtools)

   #    require(GenomicRanges)

-  if(class(LoadFile) == "GRanges"){

+  if(sum(class(LoadFile) == "GRanges")) {

     RegionRanges <- LoadFile

     if(simplify){

       RegionRanges <- GRanges(seqnames(RegionRanges),ranges(RegionRanges))

     }

   }else{

-    if(class(LoadFile) == "character"){

+    if(sum(class(LoadFile) == "character")){

       RangesTable <- read.delim(LoadFile,sep=sepr,header=TRUE,comment.char="#")

-    }else if(class(LoadFile) == "matrix"){

+    } else if(sum(class(LoadFile) == "matrix")) {

       RangesTable <- as.data.frame(LoadFile)

     } else{

       RangesTable <- as.data.frame(LoadFile)

@@ -6,7 +6,7 @@ listadd = function(a,b){

 }

 list2matrix = function(vlist,bNAasZero=TRUE) {

-   if(class(vlist)=="list"){

+   if(sum(class(vlist)=="list")){

       maxlen = max(sapply(vlist,length))

       vlist = lapply(vlist,function(x){extend(x,maxlen,bNAasZero)})

       res = matrix(0,maxlen,length(vlist))

@@ -16,7 +16,7 @@ list2matrix = function(vlist,bNAasZero=TRUE) {

       colnames(res) = names(vlist)

       rownames(res) = 1:nrow(res)

       return(res)

-   }else{

+   } else {

       return(vlist)

    }

 }

@@ -2,6 +2,12 @@

 \title{ChIPQC News}

 \encoding{UTF-8}

+\section{Version 1.13.2}{

+ \itemize{

+  \item{Fix build issue}

+  }

+}

+

 \section{Version 1.13.2}{

  \itemize{

   \item{Fixed bug when specifying consensus peakset as GRanges}