@@ -1,10 +1,7 @@

 #' Get methylation data

 #' @keywords internal

-#'

 #' @param object the object.

-#'

 #' @return the path to the methylation data.

-#'

 #' @examples

 #' showMethods("methy")

 #'

@@ -21,17 +18,8 @@ setGeneric("methy<-", function(object, value) {

 })

 #' Get sample annotation

-#'

-#' @param object the object.

-#'

-#' @return the sample annotation.

-#'

-#' @examples

-#' showMethods("samples")

-#'

-#' @export

-#'

 #' @keywords internal

+#' @export

 setGeneric("samples", valueClass = "data.frame", function(object) {

     standardGeneric("samples")

 })

@@ -45,14 +33,6 @@ setGeneric("samples<-", function(object, value) {

 #' Get exon annotation

 #' @keywords internal

-#'

-#' @param object the object.

-#'

-#' @return the exon annotation.

-#'

-#' @examples

-#' showMethods("exons")

-#'

 #' @export

 setGeneric("exons", valueClass = "data.frame", function(object) {

     standardGeneric("exons")

@@ -65,7 +45,9 @@ setGeneric("exons<-", function(object, value) {

     standardGeneric("exons<-")

 })

-#' Plot gene

+#' 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.

@@ -82,6 +64,8 @@ setGeneric("plot_gene", function(x, 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

@@ -93,7 +77,9 @@ setGeneric("plot_gene_heatmap", function(x, gene, ...) {

     standardGeneric("plot_gene_heatmap")

 })

-#' Plot region

+#' Plot region methylation

+#'

+#' Plot the methylation of a genomic region.

 #'

 #' @param x the NanoMethResult or ModBamResult object.

 #' @param chr the chromosome to plot.

@@ -112,6 +98,8 @@ setGeneric("plot_region", function(x, chr, start, end, ...) {

 #' 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.

@@ -14,8 +14,8 @@ setClass(

 #' This function creates a ModBamFiles object containing information about the

 #' samples and file paths.

 #'

-#' @param samples A character vector with the names of the samples.

-#' @param paths A character vector with the file paths for the BAM files.

+#' @param samples a character vector with the names of the samples.

+#' @param paths a character vector with the file paths for the BAM files.

 #'

 #' @return A ModBamFiles object with the sample and path information.

 #'

@@ -31,6 +31,10 @@ ModBamFiles <- function(samples, paths) {

     new("ModBamFiles", x)

 }

+#' @docType methods

+#' @rdname ModBamFiles

+#'

+#' @param object a ModBamFiles object.

 #' @export

 setMethod("show", signature("ModBamFiles"), function(object) {

     print(glue::glue(

@@ -1,5 +1,9 @@

 #' Load an example NanoMethResult object

 #'

+#' Load an example NanoMethResult object for demonstration of plotting

+#' functions. Run `load_example_nanomethresults` without the function call to

+#' see how the object is constructed.

+#'

 #' @return a NanoMethResults object

 #'

 #' @export

@@ -1,15 +1,21 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/ModBamResults.R

+\docType{methods}

 \name{ModBamFiles}

 \alias{ModBamFiles}

+\alias{show,ModBamFiles-method}

 \title{Constructor for a ModBamFiles object}

 \usage{

 ModBamFiles(samples, paths)

+

+\S4method{show}{ModBamFiles}(object)

 }

 \arguments{

-\item{samples}{A character vector with the names of the samples.}

+\item{samples}{a character vector with the names of the samples.}

+

+\item{paths}{a character vector with the file paths for the BAM files.}

-\item{paths}{A character vector with the file paths for the BAM files.}

+\item{object}{a ModBamFiles object.}

 }

 \value{

 A ModBamFiles object with the sample and path information.

@@ -6,17 +6,7 @@

 \usage{

 exons(object)

 }

-\arguments{

-\item{object}{the object.}

-}

-\value{

-the exon annotation.

-}

 \description{

 Get exon annotation

-}

-\examples{

-showMethods("exons")

-

 }

 \keyword{internal}

@@ -4,7 +4,7 @@

 \alias{plot_gene}

 \alias{plot_gene,NanoMethResult,character-method}

 \alias{plot_gene,ModBamResult,character-method}

-\title{Plot gene}

+\title{Plot gene methylation}

 \usage{

 plot_gene(x, gene, ...)

@@ -39,7 +39,7 @@ plot_gene(x, gene, ...)

 )

 }

 \arguments{

-\item{x}{the NanoMethResult object.}

+\item{x}{the NanoMethResult or ModBamResult object.}

 \item{gene}{the gene symbol for the gene to plot.}

@@ -78,7 +78,7 @@ a patchwork plot containing the methylation profile in the specified

 region.

 }

 \description{

-Plot gene

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

 }

 \section{Functions}{

 \itemize{

@@ -3,6 +3,7 @@

 \name{plot_gene_heatmap}

 \alias{plot_gene_heatmap}

 \alias{plot_gene_heatmap,NanoMethResult,character-method}

+\alias{plot_gene_heatmap,ModBamResult,character-method}

 \title{Plot gene methylation heatmap}

 \usage{

 plot_gene_heatmap(x, gene, ...)

@@ -14,9 +15,17 @@ plot_gene_heatmap(x, gene, ...)

   pos_style = c("to_scale", "compact"),

   subsample = 50

 )

+

+\S4method{plot_gene_heatmap}{ModBamResult,character}(

+  x,

+  gene,

+  window_prop = 0.3,

+  pos_style = c("to_scale", "compact"),

+  subsample = 50

+)

 }

 \arguments{

-\item{x}{the NanoMethResult object.}

+\item{x}{the NanoMethResult or ModBamResult object.}

 \item{gene}{the gene symbol for the gene to plot.}

@@ -39,7 +48,7 @@ a ggplot object of the heatmap

 a ggplot plot containing the heatmap.

 }

 \description{

-Plot gene methylation heatmap

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

 }

 \examples{

 nmr <- load_example_nanomethresult()

@@ -3,9 +3,10 @@

 \name{plot_region}

 \alias{plot_region}

 \alias{plot_region,NanoMethResult,character,numeric,numeric-method}

+\alias{plot_region,ModBamResult,character,numeric,numeric-method}

 \alias{plot_region,NanoMethResult,factor,numeric,numeric-method}

 \alias{plot_region,ModBamResult,factor,numeric,numeric-method}

-\title{Plot region}

+\title{Plot region methylation}

 \usage{

 plot_region(x, chr, start, end, ...)

@@ -25,6 +26,22 @@ plot_region(x, chr, start, end, ...)

   line_size = 2

 )

+\S4method{plot_region}{ModBamResult,character,numeric,numeric}(

+  x,

+  chr,

+  start,

+  end,

+  anno_regions = NULL,

+  binary_threshold = NULL,

+  avg_method = c("mean", "median"),

+  spaghetti = FALSE,

+  heatmap = FALSE,

+  span = NULL,

+  window_prop = 0,

+  palette = ggplot2::scale_colour_brewer(palette = "Set1"),

+  line_size = 2

+)

+

 \S4method{plot_region}{NanoMethResult,factor,numeric,numeric}(

   x,

   chr,

@@ -58,7 +75,7 @@ plot_region(x, chr, start, end, ...)

 )

 }

 \arguments{

-\item{x}{the NanoMethResult object.}

+\item{x}{the NanoMethResult or ModBamResult object.}

 \item{chr}{the chromosome to plot.}

@@ -99,7 +116,7 @@ a patchwork plot containing the methylation profile in the specified

 region.

 }

 \description{

-Plot region

+Plot the methylation of a genomic region.

 }

 \examples{

 nmr <- load_example_nanomethresult()

@@ -3,7 +3,9 @@

 \name{plot_region_heatmap}

 \alias{plot_region_heatmap}

 \alias{plot_region_heatmap,NanoMethResult,character,numeric,numeric-method}

+\alias{plot_region_heatmap,ModBamResult,character,numeric,numeric-method}

 \alias{plot_region_heatmap,NanoMethResult,factor,numeric,numeric-method}

+\alias{plot_region_heatmap,ModBamResult,factor,numeric,numeric-method}

 \title{Plot region methylation heatmap}

 \usage{

 plot_region_heatmap(x, chr, start, end, ...)

@@ -18,6 +20,16 @@ plot_region_heatmap(x, chr, start, end, ...)

   subsample = 50

 )

+\S4method{plot_region_heatmap}{ModBamResult,character,numeric,numeric}(

+  x,

+  chr,

+  start,

+  end,

+  pos_style = c("to_scale", "compact"),

+  window_prop = 0,

+  subsample = 50

+)

+

 \S4method{plot_region_heatmap}{NanoMethResult,factor,numeric,numeric}(

   x,

   chr,

@@ -27,9 +39,19 @@ plot_region_heatmap(x, chr, start, end, ...)

   window_prop = 0,

   subsample = 50

 )

+

+\S4method{plot_region_heatmap}{ModBamResult,factor,numeric,numeric}(

+  x,

+  chr,

+  start,

+  end,

+  pos_style = c("to_scale", "compact"),

+  window_prop = 0,

+  subsample = 50

+)

 }

 \arguments{

-\item{x}{the NanoMethResult object.}

+\item{x}{the NanoMethResult or ModBamResult object.}

 \item{chr}{the chromosome to plot.}

@@ -56,7 +78,7 @@ a ggplot object of the heatmap.

 a ggplot plot containing the heatmap.

 }

 \description{

-Plot region methylation heatmap

+Plot the methylation heatmap of a genomic region.

 }

 \examples{

 nmr <- load_example_nanomethresult()

@@ -6,17 +6,7 @@

 \usage{

 samples(object)

 }

-\arguments{

-\item{object}{the object.}

-}

-\value{

-the sample annotation.

-}

 \description{

 Get sample annotation

-}

-\examples{

-showMethods("samples")

-

 }

 \keyword{internal}