# Generated by roxygen2: do not edit by hand

export(A)
export(AUC)
export(K)
export(N)
export(R)
export(annotatedData)
export(betaHMM)
export(betaHMMResults)
export(betaHMMrun)
export(chromosome_number)
export(dmcResults)
export(dmc_identification)
export(dmc_identification_run)
export(dmrResults)
export(dmr_identification)
export(dmr_identification_run)
export(hidden_states)
export(llk)
export(model_parameters)
export(phi)
export(plot)
export(summary)
export(tau)
export(threshold)
export(threshold_Results)
export(threshold_identification)
export(threshold_identification_run)
export(treatment_group)
export(uncertainty)
exportClasses(betaHMMResults)
exportClasses(dmcResults)
exportClasses(dmrResults)
exportClasses(threshold_Results)
exportMethods(A)
exportMethods(AUC)
exportMethods(K)
exportMethods(N)
exportMethods(R)
exportMethods(annotatedData)
exportMethods(betaHMM)
exportMethods(chromosome_number)
exportMethods(dmc_identification)
exportMethods(dmr_identification)
exportMethods(hidden_states)
exportMethods(llk)
exportMethods(model_parameters)
exportMethods(phi)
exportMethods(plot)
exportMethods(summary)
exportMethods(tau)
exportMethods(threshold)
exportMethods(threshold_identification)
exportMethods(treatment_group)
exportMethods(uncertainty)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)
importFrom(GenomicRanges,mcols)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(cowplot,plot_grid)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,mutate)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(pROC,auc)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(scales,seq_gradient_pal)
importFrom(stats,C)
importFrom(stats,complete.cases)
importFrom(stats,dbeta)
importFrom(stats,density)
importFrom(stats,kmeans)
importFrom(stats,p.adjust)
importFrom(stats,rbeta)
importFrom(stats,sd)
importFrom(stringr,str_split)
importFrom(tidyr,"%>%")
importFrom(tidyr,pivot_longer)
importFrom(tidyselect,all_of)
importFrom(utils,tail)
importMethodsFrom(S4Vectors,metadata)