S3method(print,hapNet)
S3method(print,hapResult)
S3method(print,hapSummary)
export(addINFO)
export(addPromoter)
export(as.haplotype)
export(displayVarOnGeneModel)
export(filterLargeVCF)
export(filterLargeP.link)
export(filter_hap)
export(filter_hmp)
export(filter_plink.pedmap)
export(filter_table)
export(filter_vcf)
export(getGenePOS)
export(getGeneRanges)
export(getHapGroup)
export(get_hapNet)
export(gffSetATGas0)
export(hap2hmp)
export(hapDistribution)
export(hapSetATGas0)
export(hapVsPheno)
export(hapVsPhenos)
export(hap_summary)
export(hmp2hap)
export(import_AccINFO)
export(import_MultipleAlignment)
export(import_bed)
export(import_gff)
export(import_hap)
export(import_plink.pedmap)
export(import_seqs)
export(import_vcf)
export(plink.pedmap2hap)
export(plotEFF)
export(plotHapNet)
export(plotHapTable)
export(plot_LDheatmap)
export(seqs2hap)
export(siteEFF)
export(sites)
export(table2hap)
export(trimSeqs)
export(vcf2hap)
export(write.hap)
import(ggplot2)
import(grDevices)
import(grid)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,as.matrix)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,width)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,as.data.frame)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,`%over%`)
importFrom(IRanges,end)
importFrom(IRanges,start)
importFrom(ape,as.DNAbin)
importFrom(genetics,LD)
importFrom(genetics,as.genotype)
importFrom(genetics,is.genotype)
importFrom(genetics,nallele)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,locator)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(maps,map)
importFrom(methods,as)
importFrom(pegas,haploNet)
importFrom(rlang,.data)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(stats,IQR)
importFrom(stats,chisq.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,shapiro.test)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(stringdist,stringdist)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_length)
importFrom(stringr,str_pad)
importFrom(stringr,str_starts)
importFrom(tibble,tibble)
importFrom(tidyr,`%>%`)
importFrom(tidyr,chop)
importFrom(tidyr,matches)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(lolliplot,lolliplot)
importFrom(utils, head)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)
importFrom(vcfR,extract_gt_tidy)
importFrom(vcfR,getALT)
importFrom(vcfR,getCHROM)
importFrom(vcfR,getINFO)
importFrom(vcfR,getPOS)
importFrom(vcfR,getREF)
importFrom(vcfR,is.biallelic)
importFrom(vcfR,is.indel)
importFrom(vcfR,read.vcfR)



if(tools:::.OStype() == "windows"){
    importFrom(shiny, HTML)
    importFrom(shiny, actionButton)
    importFrom(shiny, br)
    importFrom(shiny, checkboxGroupInput)
    importFrom(shiny, checkboxInput)
    importFrom(shiny, column)
    importFrom(shiny, eventReactive)
    importFrom(shiny, fluidPage)
    importFrom(shiny, fluidRow)
    importFrom(shiny, h1)
    importFrom(shiny, h3)
    importFrom(shiny, h4)
    importFrom(shiny, htmlOutput)
    importFrom(shiny, mainPanel)
    importFrom(shiny, navbarPage)
    importFrom(shiny, navlistPanel)
    importFrom(shiny, numericInput)
    importFrom(shiny, observeEvent)
    importFrom(shiny, p)
    importFrom(shiny, plotOutput)
    importFrom(shiny, radioButtons)
    importFrom(shiny, reactive)
    importFrom(shiny, renderPlot)
    importFrom(shiny, renderPrint)
    importFrom(shiny, renderTable)
    importFrom(shiny, renderUI)
    importFrom(shiny, runApp)
    importFrom(shiny, selectInput)
    importFrom(shiny, shinyApp)
    importFrom(shiny, sidebarPanel)
    importFrom(shiny, sliderInput)
    importFrom(shiny, tabPanel)
    importFrom(shiny, tabPanelBody)
    importFrom(shiny, tableOutput)
    importFrom(shiny, tabsetPanel)
    importFrom(shiny, textInput)
    importFrom(shiny, textOutput)
    importFrom(shiny, titlePanel)
    importFrom(shiny, updateActionButton)
    importFrom(shiny, updateCheckboxGroupInput)
    importFrom(shiny, updateNumericInput)
    importFrom(shiny, updateRadioButtons)
    importFrom(shiny, updateSelectInput)
    importFrom(shiny, updateTextInput)
    importFrom(shiny, verbatimTextOutput)
    importFrom(utils,choose.dir)
    importFrom(utils,choose.files)
    importFrom(utils,read.csv)
    importFrom(shinyjs,hidden)
    importFrom(shinyjs,hide)
    importFrom(shinyjs,show)
    importFrom(shinyjs,toggle)
    importFrom(shinyjs, useShinyjs)
    export(build_app_geneHapR)
    export(startGUI.geneHapR)
}
