@@ -6,7 +6,6 @@ Author: Divy Kangeyan <[email protected]>

 Maintainer: Divy Kangeyan <[email protected]>

 Depends: R (>= 3.5.0)

 Imports:

-  ggplot2,

   knitr,

   rmarkdown,

   bsseq,

@@ -22,7 +21,6 @@ Imports:

   GenomeInfoDb,

   Biostrings,

   DT,

-  ggthemes,

   scales,

   viridis,

   HDF5Array (>= 1.7.5)

@@ -32,7 +30,9 @@ Suggests:

   TxDb.Hsapiens.UCSC.hg38.knownGene,

   org.Hs.eg.db,

   Biobase,

-  BiocGenerics

+  BiocGenerics,

+  ggplot2,

+  ggthemes

 Description: Functions to analyze methylation data can be found here.

              Some functions are relevant for single cell methylation data but most other

              functions can be used for any  methylation data.

@@ -215,7 +215,7 @@ g

 ## Feature level coverage

 ```{r feature_coverage,echo=FALSE,warning=FALSE,message=FALSE,fig.height=5, fig.width=5, eval=TRUE ,fig.align='center'}

-library(annotatr)

+#library(annotatr)

 featureCovMatrix <- scmeth::featureCoverage(bs,c('genes_promoters','genes_exons','genes_introns','genes_intergenic','cpg_islands','cpg_shelves','cpg_shores','cpg_inter'),params$genome)

 featureCovDf <- reshape2::melt(featureCovMatrix)