# Generated by roxygen2: do not edit by hand

export(ASM)
export(extract_bam_regions)
export(prepare_cpg_snp_input)
export(run_pipeline)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBam)
importFrom(data.table,":=")
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,fcase)
importFrom(data.table,fifelse)
importFrom(data.table,foverlaps)
importFrom(data.table,fread)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(data.table,uniqueN)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(readxl,read_xlsx)
importFrom(stats,sd)
importFrom(utils,capture.output)
importFrom(utils,head)
importFrom(utils,write.table)
importFrom(vcfR,extract.gt)
importFrom(vcfR,read.vcfR)
importFrom(writexl,write_xlsx)
