#' Get methylation data
 #' @keywords internal
 #' @param object the object.
 #' @return the path to the methylation data.
 #' @examples
 #' showMethods("methy")
 #'
 #' @export

 setGeneric("methy", valueClass = "ANY", function(object) {

     standardGeneric("methy")
 })
 
 #' Set methylation data
 #' @keywords internal
 #' @export
 setGeneric("methy<-", function(object, value) {
     standardGeneric("methy<-")
 })
 
 #' Get sample annotation
 #' @keywords internal

 #' @export

 setGeneric("samples", valueClass = "data.frame", function(object) {
     standardGeneric("samples")
 })
 
 #' Set sample annotation
 #' @keywords internal
 #' @export
 setGeneric("samples<-", function(object, value) {
     standardGeneric("samples<-")
 })
 
 #' Get exon annotation
 #' @keywords internal
 #' @export
 setGeneric("exons", valueClass = "data.frame", function(object) {
     standardGeneric("exons")
 })
 
 #' Set exon annotation
 #' @keywords internal
 #' @export
 setGeneric("exons<-", function(object, value) {
     standardGeneric("exons<-")
 })
 

 #' Get mod code
 #' @keywords internal
 #' @export
 setGeneric("mod_code", valueClass = "character", function(object) {
     standardGeneric("mod_code")
 })
 
 #' Set mod code
 #' @keywords internal
 #' @export
 setGeneric("mod_code<-", function(object, value) {
     standardGeneric("mod_code<-")
 })
 

 #' Plot gene methylation
 #'
 #' Plot the methylation of a gene symbol specified within the exon(x) slot.

 #'

 #' @param x the NanoMethResult or ModBamResult object.

 #' @param gene the gene symbol for the gene to plot.

 #' @param ... additional arguments.

 #'
 #' @return a patchwork plot containing the methylation profile in the specified
 #'   region.
 #'
 #' @importFrom ggrastr rasterise
 #' @export
 setGeneric("plot_gene", function(x, gene, ...) {
     standardGeneric("plot_gene")
 })
 
 #' Plot gene methylation heatmap
 #'

 #' Plot the methylation heatmap of a gene symbol specified within the exon(x) slot.
 #'

 #' @param x the NanoMethResult or ModBamResult object.

 #' @param gene the gene symbol for the gene to plot.

 #' @param ... additional arguments.

 #'
 #' @return a ggplot object of the heatmap
 #'
 #' @export
 setGeneric("plot_gene_heatmap", function(x, gene, ...) {
     standardGeneric("plot_gene_heatmap")
 })
 

 #' Plot region methylation
 #'
 #' Plot the methylation of a genomic region.

 #'

 #' @param x the NanoMethResult or ModBamResult object.

 #' @param chr the chromosome to plot.
 #' @param start the start of the plotting region.
 #' @param end the end of the plotting region.

 #' @param ... additional arguments.

 #'
 #' @return a patchwork plot containing the methylation profile in the specified
 #'   region.
 #'
 #' @importFrom ggrastr rasterise
 #' @export
 setGeneric("plot_region", function(x, chr, start, end, ...) {
     standardGeneric("plot_region")
 })
 
 #' Plot region methylation heatmap
 #'

 #' Plot the methylation heatmap of a genomic region.
 #'

 #' @param x the NanoMethResult or ModBamResult object.

 #' @param chr the chromosome to plot.
 #' @param start the start of the plotting region.
 #' @param end the end of the plotting region.

 #' @param ... additional arguments.

 #'
 #' @return a ggplot object of the heatmap.
 #'
 #' @export
 setGeneric("plot_region_heatmap", function(x, chr, start, end, ...) {
     standardGeneric("plot_region_heatmap")
 })