# Generated by roxygen2: do not edit by hand

S3method(qtleEstimate,QTLExperiment)
S3method(qtleEstimate,list)
export("callSignificance<-")
export(callSignificance)
export(getComplete)
export(getSignificant)
export(getTopHits)
export(plotCompareStates)
export(plotPairwiseSharing)
export(plotQTLClusters)
export(plotSimulationParams)
export(plotUpSet)
export(qtleEstimate)
export(qtleParams)
export(qtleParams2)
export(qtleSimulate)
export(replaceNAs)
export(runPairwiseSharing)
export(runSignificantFeatures)
export(runTestMetrics)
export(simPerformance)
exportMethods(callSignificance)
import(QTLExperiment)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,UpSet)
importFrom(ComplexHeatmap,comb_degree)
importFrom(ComplexHeatmap,comb_size)
importFrom(ComplexHeatmap,make_comb_mat)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(ComplexHeatmap,set_size)
importFrom(QTLExperiment,QTLExperiment)
importFrom(QTLExperiment,betas)
importFrom(QTLExperiment,errors)
importFrom(QTLExperiment,mockQTLE)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(circlize,colorRamp2)
importFrom(collapse,fmutate)
importFrom(collapse,na_omit)
importFrom(data.table,.SD)
importFrom(data.table,setDT)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,select)
importFrom(dplyr,slice_min)
importFrom(dplyr,starts_with)
importFrom(fitdistrplus,fitdist)
importFrom(ggplot2,.data)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_brewer)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(grDevices,hcl.colors)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(mashr,mash_1by1)
importFrom(mashr,mash_set_data)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(methods,is)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,rgamma)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(tidyr,pivot_longer)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_fill_viridis)
importFrom(viridis,viridis)
