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

 Package: scmeth

 Type: Package

 Title: Functions to conduct quality control analysis in methylation data

-Version: 1.3.0

+Version: 1.3.1

 Author: Divy Kangeyan <[email protected]>

 Maintainer: Divy Kangeyan <[email protected]>

 Depends: R (>= 3.5.0)

@@ -14,7 +14,7 @@

 #'@examples

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

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

-#'featureCoverage(bs, c('cpg_islands', 'genes_exons'), 'hg38')

+#'featureCoverage(bs, c('cpg_islands', 'cpg_shores'), 'hg38')

 #'@importFrom DelayedArray rowSums

 #'@importFrom GenomeInfoDb seqlevelsStyle

 #'@importFrom annotatr builtin_genomes

@@ -28,5 +28,5 @@ by the user

 \examples{

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

 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

-featureCoverage(bs, c('cpg_islands', 'genes_exons'), 'hg38')

+featureCoverage(bs, c('cpg_islands', 'cpg_shores'), 'hg38')

 }

@@ -44,5 +44,5 @@ directory <- system.file("extdata/bismark_data", package='scmeth')

 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

 mbiasDirectory=system.file("extdata", package='scmeth')

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

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

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

 }

@@ -197,7 +197,7 @@ that region.

 </p>

 ```{r, warning=FALSE,message=FALSE}

 #library(annotatr)

-featureList <- c('genes_exons', 'genes_introns')

+featureList <- c('cpg_islands', 'cpg_shores', 'cpg_shelves')

 DT::datatable(featureCoverage(bsObject, features=featureList, "hg38"))

 ```

 </p>