@@ -15,7 +15,6 @@ Imports:

   stats,

   utils,

   BSgenome,

-  DelayedArray

 Suggests:

   rmarkdown,

   BSgenome.Mmusculus.UCSC.mm10,

@@ -7,10 +7,10 @@

 #'load(system.file("extdata",'bsObject.rda',package='scmeth'))

 #'coverage(bs)

 #'@export

-#'@importFrom DelayedArray colSums

+

 coverage <- function(bs) {

     covMatrix<-bsseq::getCoverage(bs)

-    covVec<- DelayedArray::colSums(covMatrix>0,na.rm=TRUE)

+    covVec<- colSums(covMatrix>0,na.rm=TRUE)

     return(covVec)

 }

@@ -10,7 +10,7 @@

 #'cpgDensity(bs,Mmusculus,1000)

 #'@import BSgenome

 #'@export

-#'@importFrom DelayedArray colSums

+

 cpgDensity<-function(bs,organism,windowLength=1000){

@@ -22,7 +22,7 @@ cpgDensity<-function(bs,organism,windowLength=1000){

     }else{

         cpgdBin<-cut(cpgd,c(seq(0,20),max(cpgd)))

     }

-    cpgdCov <- by(cov>0, cpgdBin, DelayedArray::colSums)

+    cpgdCov <- by(cov>0, cpgdBin, colSums)

     cpgdCov <- do.call("rbind", cpgdCov)

     return(cpgdCov)

 }

@@ -16,7 +16,7 @@

 #'load(system.file("extdata",'bsObject.rda',package='scmeth'))

 #'cpgDiscretization(bs)

 #'@export

-#'@importFrom DelayedArray colSums

+

 cpgDiscretization<-function(bs){

     covMatrix<-as.matrix(bsseq::getCoverage(bs))

@@ -25,7 +25,7 @@ cpgDiscretization<-function(bs){

     tempMethylationMatrix<-methMatrix

     methMatrix[methMatrix<=0.2]<-0

     methMatrix[methMatrix>=0.8]<-1

-    removedCpGs<-DelayedArray::colSums(methMatrix>0.2 & methMatrix<0.8, na.rm=TRUE)

+    removedCpGs<-colSums(methMatrix>0.2 & methMatrix<0.8, na.rm=TRUE)

     removedCpGFrac<-(removedCpGs/(scmeth::coverage(bs)))*100

     returnList<-list('meth' = methMatrix, 'discard' = removedCpGs,

                    'discard-perc' = removedCpGFrac)

@@ -11,7 +11,7 @@

 #'load(system.file("extdata",'bsObject.rda',package='scmeth'))

 #'repMask(bs,Mmusculus,'mm10')

 #'@export

-#'@importFrom DelayedArray colSums

+

 repMask<-function(bs,organism,genome){

     hub <- AnnotationHub::AnnotationHub()

@@ -19,6 +19,6 @@ repMask<-function(bs,organism,genome){

                        c("rmsk", GenomeInfoDb::organism(organism), genome)))]]

     rep <- GenomicRanges::countOverlaps(bs, repeatGr)>0

     cov<-bsseq::getCoverage(bs)

-    covDf <- data.frame(coveredCpgs=DelayedArray::colSums(cov[!rep,]>=1))

+    covDf <- data.frame(coveredCpgs=colSums(cov[!rep,]>=1))

     return(covDf)

 }