@@ -28,13 +28,10 @@ importFrom(annotatr,build_annotations)

 importFrom(annotatr,builtin_genomes)

 importFrom(annotatr,summarize_annotations)

 importFrom(bsseq,getCoverage)

-importFrom(ggthemes,theme_tufte)

 importFrom(scales,comma)

 importFrom(stats,aggregate)

 importFrom(stats,dbinom)

-importFrom(stats,relevel)

 importFrom(stats,sd)

 importFrom(utils,read.csv)

-importFrom(utils,read.delim)

 importFrom(utils,read.table)

 importFrom(viridis,scale_fill_viridis)

@@ -17,13 +17,5 @@ bsConversionPlot <- function(bs){

                                     (phenoData$CHH_meth+phenoData$CHH_unmeth+

                                     phenoData$CHG_meth+phenoData$CHG_unmeth)

     bscDf <- data.frame(sample=rownames(phenoData),bsc=phenoData$bsconversion)

-

-    #g <- ggplot2::ggplot(bscDf, ggplot2::aes_string(x="''", y='bsc'))

-    #g <- g+ggplot2::geom_boxplot()

-    #g <- g+ggplot2::ylim(max(min(bscDf$bsc)-0.02,0),min(max(bscDf$bsc)+0.02,1))

-    #g <- g+ggplot2::theme_bw()

-    #g <- g+ggplot2::geom_jitter()

-    #g <- g+ggplot2::xlab('')+ggplot2::ylab('bisulfite conversion rate')

-    #g <- g+ggplot2::ggtitle('Bisulfite conversion rate across samples')

     return(bscDf)

 }

@@ -18,7 +18,7 @@

 #'@examples

 #'directory <- system.file("extdata/bismark_data",package='scmeth')

 #'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

-#'downsample(bs)

+#'scmeth::downsample(bs)

 #'@importFrom stats dbinom

 #'@importFrom bsseq getCoverage

 #'

@@ -15,7 +15,6 @@

 #'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

 #'methylationDist(bs)

 #'@importFrom bsseq getCoverage

-#'@importFrom ggthemes theme_tufte

 #'@export

@@ -8,8 +8,6 @@

 #'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

 #'readmetrics(bs)

 #'@export

-#'@importFrom utils read.delim

-#'@importFrom stats relevel

 readmetrics <- function(bs){

@@ -26,7 +26,6 @@

 #'outDir <- system.file(package='scmeth')

 #'report(bs,outDir,Hsapiens,'hg38',mbiasDir=mbiasDirectory,small=TRUE)

 #'@importFrom scales comma

-#'@importFrom scales comma

 #'@importFrom viridis scale_fill_viridis

 #'@importFrom HDF5Array loadHDF5SummarizedExperiment

 #'@import knitr

@@ -34,5 +34,5 @@ Downsample the CpG coverage matrix for saturation analysis

 \examples{

 directory <- system.file("extdata/bismark_data",package='scmeth')

 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

-downsample(bs)

+scmeth::downsample(bs)

 }

@@ -239,7 +239,7 @@ report renders this information into a plot. Downsampling rate ranges from

 </p>

 ```{r,warning=FALSE}

-#DT::datatable(downsample(bsObject))

+DT::datatable(scmeth::downsample(bsObject))

 ```