# Generated by roxygen2: do not edit by hand

S3method(df.residual,imputed_model)
S3method(df.residual,rlm)
S3method(sigma,imputed_model)
S3method(sigma,rlm)
S3method(stats::df.residual,rfit_prolfqua)
S3method(stats::sigma,rfit_prolfqua)
S3method(stats::vcov,rfit_prolfqua)
S3method(vcov,imputed_model)
export(AggregateLimpa)
export(AggregateMedpolish)
export(AggregateRlm)
export(AggregateTopN)
export(AnalysisConfiguration)
export(AnovaExtractor)
export(ContrastConfiguration)
export(Contrasts)
export(ContrastsBinomialFirthNestedFacade)
export(ContrastsBinomialNestedFacade)
export(ContrastsDEqMSFacade)
export(ContrastsDEqMSVoomFacade)
export(ContrastsFacadeBase)
export(ContrastsFirth)
export(ContrastsFirthFacade)
export(ContrastsFirthNestedFacade)
export(ContrastsHurdleFacade)
export(ContrastsHurdleNestedFacade)
export(ContrastsInterface)
export(ContrastsLMFacade)
export(ContrastsLMImputeFacade)
export(ContrastsLimma)
export(ContrastsLimmaFacade)
export(ContrastsLimmaImputeFacade)
export(ContrastsLimmaVoomFacade)
export(ContrastsLimmaVoomImputeFacade)
export(ContrastsLimpaFacade)
export(ContrastsLimpaNestedFacade)
export(ContrastsLmerNestedFacade)
export(ContrastsModerated)
export(ContrastsModeratedDEqMS)
export(ContrastsPlotter)
export(ContrastsRLMFacade)
export(ContrastsROPECA)
export(ContrastsROPECANestedFacade)
export(ContrastsRfitFacade)
export(ContrastsRfitImputeFacade)
export(ContrastsTable)
export(FACADE_REGISTRY)
export(HierarchyCountsSample)
export(LFQData)
export(LFQDataPlotter)
export(LFQDataStats)
export(LFQDataSummariser)
export(LFQDataToSummarizedExperiment)
export(LFQDataTransformer)
export(LR_test)
export(MissingHelpers)
export(Model)
export(ModelFirth)
export(ModelInterface)
export(ModelLimma)
export(R6_extract_values)
export(StrategyBinomial)
export(StrategyBinomialFirth)
export(StrategyLM)
export(StrategyLimma)
export(StrategyLimpa)
export(StrategyLmer)
export(StrategyLogistf)
export(StrategyRLM)
export(StrategyRfit)
export(adjust_p_values)
export(aggregate_intensity_top_n)
export(annotation_add_contrasts)
export(apply_to_response_matrix)
export(build_contrast_analysis)
export(build_model)
export(build_model_glm_peptide)
export(build_model_glm_protein)
export(build_model_impute)
export(build_model_limma)
export(build_model_limma_impute)
export(build_model_limma_voom)
export(build_model_limma_voom_impute)
export(build_model_limpa)
export(build_model_logistf)
export(center_to_reference_cfg)
export(complete_cases)
export(compute_contrast)
export(compute_lmer_contrast)
export(compute_pooled)
export(contrasts_linfct)
export(encode_bin_resp)
export(estimate_intensity)
export(find_package_file)
export(generate_contrasts)
export(generate_contrasts_for_factor)
export(get_anova_df)
export(get_complete_model_fit)
export(get_contrast)
export(get_p_values_pbeta)
export(get_robscales)
export(get_uniprot_id_from_fasta_header)
export(group_label)
export(hierarchy_counts)
export(impute_from_model)
export(interaction_contrasts)
export(is_contaminant)
export(is_decoy)
export(level_specific_contrasts)
export(lfq_power_t_test_proteins)
export(lfq_power_t_test_quantiles_V2)
export(linfct_from_model)
export(linfct_matrix_contrasts)
export(list_facades)
export(list_to_AnalysisConfiguration)
export(list_to_ContrastConfiguration)
export(lookup_facade)
export(main_effect_contrasts)
export(make_interaction_column)
export(make_reduced_hierarchy_config)
export(matrix_to_tibble)
export(merge_contrasts_results)
export(missigness_histogram)
export(missingness_per_condition)
export(missingness_per_condition_cumsum)
export(model_analyse)
export(model_summary)
export(moderated_p_deqms)
export(moderated_p_deqms_long)
export(moderated_p_limma)
export(multigroup_volcano)
export(nr_children_experiment)
export(nr_features_experiment)
export(nr_obs_sample)
export(pairs_smooth)
export(panel_cor)
export(pivot_model_contrasts_to_wide)
export(plot_estimate)
export(plot_heatmap)
export(plot_heatmap_cor)
export(plot_hierarchies_boxplot)
export(plot_hierarchies_boxplot_df)
export(plot_hierarchies_line)
export(plot_intensity_distribution_density)
export(plot_intensity_distribution_violin)
export(plot_na_heatmap)
export(plot_pca)
export(plot_raster)
export(plot_sample_correlation)
export(plot_stat_density)
export(plot_stat_density_median)
export(plot_stat_violin)
export(plot_stat_violin_median)
export(plot_stdv_vs_mean)
export(poolvar)
export(prolfqua_data)
export(rank_peptide_by_intensity)
export(register_facade)
export(response_matrix_as_tibble)
export(robust_scale)
export(sample_subset)
export(scale_with_subset)
export(script_copy_helper_vec)
export(separate_hierarchy)
export(setup_analysis)
export(sim_build_models_lm)
export(sim_build_models_lmer)
export(sim_build_models_logistf)
export(sim_lfq_data)
export(sim_lfq_data_2factor_config)
export(sim_lfq_data_peptide_config)
export(sim_lfq_data_protein_config)
export(sim_make_model_lm)
export(sim_make_model_lmer)
export(strategy_binomial)
export(strategy_binomial_firth)
export(strategy_limma)
export(strategy_limpa)
export(strategy_lm)
export(strategy_lmer)
export(strategy_logistf)
export(strategy_rfit)
export(strategy_rlm)
export(summarize_hierarchy)
export(summarize_stats)
export(summarize_stats_factors)
export(summarize_stats_quantiles)
export(summary_ROPECA_median_p_scaled)
export(table_facade)
export(table_factors)
export(table_factors_size)
export(tidy_to_wide_config)
export(transform_work_intensity)
export(upset_interaction_missing_stats)
export(upset_missing_stats)
export(volcano_plotly)
export(which_missing)
import(dplyr)
import(ggplot2)
importFrom(ComplexHeatmap,
  Heatmap,
  HeatmapAnnotation,
  draw
)
importFrom(MASS,rlm)
importFrom(UpSetR,upset)
importFrom(circlize,colorRamp2)
importFrom(dplyr,
  across,
  all_of,
  anti_join,
  arrange,
  bind_cols,
  bind_rows,
  case_when,
  count,
  desc,
  distinct,
  filter,
  group_by,
  inner_join,
  left_join,
  mutate,
  nest_by,
  rename,
  select,
  starts_with,
  summarize,
  ungroup
)
importFrom(forcats,fct_relevel)
importFrom(ggplot2,
  aes,
  element_text,
  facet_grid,
  geom_boxplot,
  geom_line,
  geom_violin,
  ggplot,
  ggtitle,
  guides,
  scale_x_continuous,
  scale_y_continuous,
  stat_summary,
  theme
)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,
  colorRampPalette,
  dev.off,
  pdf,
  png,
  rainbow
)
importFrom(graphics,
  abline,
  hist,
  pairs,
  par,
  plot,
  rect,
  text
)
importFrom(limma,
  contrasts.fit,
  eBayes,
  lmFit,
  topTable
)
importFrom(logistf,logistf)
importFrom(methods,new)
importFrom(plotly,ggplotly)
importFrom(purrr,
  map,
  map2,
  map2_dbl,
  map_chr,
  map_dbl,
  map_df,
  map_dfc,
  map_if,
  map_int,
  map_lgl,
  reduce
)
importFrom(rlang,
  ":=",
  .data,
  sym,
  syms
)
importFrom(stats,
  .lm.fit,
  anova,
  approx,
  as.formula,
  coef,
  coefficients,
  confint,
  cor,
  cor.test,
  delete.response,
  df,
  df.residual,
  ecdf,
  fisher.test,
  formula,
  ftable,
  glm,
  lm,
  lm.fit,
  mad,
  median,
  medpolish,
  model.matrix,
  na.omit,
  p.adjust,
  pbeta,
  pchisq,
  pf,
  pnorm,
  power.t.test,
  prcomp,
  predict,
  pt,
  qf,
  qt,
  quantile,
  residuals,
  rgeom,
  rlnorm,
  rnorm,
  sd,
  setNames,
  sigma,
  terms,
  uniroot,
  update,
  vcov
)
importFrom(tibble,
  add_column,
  as_tibble,
  column_to_rownames,
  tibble
)
importFrom(tidyr,
  nest,
  nesting,
  pivot_longer,
  pivot_wider,
  separate,
  separate_rows,
  unite,
  unnest
)
importFrom(utils,
  combn,
  data,
  head,
  read.csv,
  tail,
  unzip
)
