# 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,
  HeatmapAnnotation,
  UpSet,
  comb_degree,
  comb_size,
  make_comb_mat,
  rowAnnotation,
  set_size
)
importFrom(QTLExperiment,
  QTLExperiment,
  betas,
  errors,
  mockQTLE
)
importFrom(S4Vectors,
  "metadata<-",
  metadata
)
importFrom(SummarizedExperiment,
  "assay<-",
  "assays<-",
  "colData<-",
  "rowData<-",
  assay,
  assays,
  colData,
  rowData
)
importFrom(circlize,colorRamp2)
importFrom(collapse,
  fmutate,
  na_omit
)
importFrom(data.table,
  .SD,
  setDT
)
importFrom(dplyr,
  "%>%",
  arrange,
  distinct,
  filter,
  group_by,
  select,
  slice_min,
  starts_with
)
importFrom(fitdistrplus,fitdist)
importFrom(ggplot2,
  .data,
  aes,
  facet_grid,
  geom_abline,
  geom_density,
  geom_point,
  ggplot,
  scale_color_brewer,
  scale_color_manual,
  scale_fill_brewer,
  scale_fill_manual,
  theme_classic,
  xlim,
  ylim
)
importFrom(grDevices,hcl.colors)
importFrom(grid,
  gpar,
  grid.text
)
importFrom(mashr,
  mash_1by1,
  mash_set_data
)
importFrom(matrixStats,
  rowMedians,
  rowMins
)
importFrom(methods,is)
importFrom(stats,
  na.omit,
  p.adjust,
  rgamma,
  rnorm,
  sd,
  setNames
)
importFrom(tidyr,pivot_longer)
importFrom(viridis,
  scale_color_viridis,
  scale_fill_viridis,
  viridis
)
