export('hiddenMarkovAnalysis')
export('summarizeRegions1')
export('summarizeRegions2')
export('regionFinalize')
export('documentErrorRegions')
export('prepareHMMdataframes')
export('regionAnalysis')
export('runHMM_1')
export('runHMM_2')
export('runHMM_3')
export('marginalLikelihoodM1')
export('marginalLikelihoodM2')
export('splitByChromosome')
export('modePeakCalc')
export('marginalM1Calc')
export('marginalM2CalcBLOH')
export('marginalM2CalcBHET')
export('removeOutlierFromCalc')
export('tLOHCalc')
export('tLOHCalcUpdate')
export('tLOHDataImport')
export('aggregateCHRPlot')
export('alleleFrequencyPlot')
importFrom(stringr, str_split)
importFrom(naniar,replace_with_na_at)
importFrom(dplyr, tibble)
importFrom(dplyr,case_when)
importFrom(dplyr, filter)
importFrom("stats","gaussian","median","quantile")
importFrom("stats", "complete.cases", "dbeta", "dbinom", "integrate","density")
importFrom("utils", "read.csv", "tail", "write.csv")
importFrom("VariantAnnotation","geno","readVcf")
importFrom("GenomicRanges","seqnames","start")
importFrom("MatrixGenerics", "rowRanges")
importFrom(bestNormalize,orderNorm)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,aes)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,annotate)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,labs)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,unit)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,element_blank)
importFrom(purrr,reduce)
import(data.table)
importFrom(dplyr, full_join)
importFrom(depmixS4, depmix)
importFrom(depmixS4,fit)
importFrom(depmixS4, posterior)