# 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(ContrastsBinomialNestedFacade)
export(ContrastsDEqMSFacade)
export(ContrastsDEqMSVoomFacade)
export(ContrastsFacadeBase)
export(ContrastsFirth)
export(ContrastsFirthFacade)
export(ContrastsFirthNestedFacade)
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(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_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)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(MASS,rlm)
importFrom(UpSetR,upset)
importFrom(circlize,colorRamp2)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,anti_join)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,nest_by)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(forcats,fct_relevel)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,theme)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,hist)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(logistf,logistf)
importFrom(methods,new)
importFrom(plotly,ggplotly)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_dbl)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_df)
importFrom(purrr,map_dfc)
importFrom(purrr,map_if)
importFrom(purrr,map_int)
importFrom(purrr,map_lgl)
importFrom(purrr,reduce)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(stats,.lm.fit)
importFrom(stats,anova)
importFrom(stats,approx)
importFrom(stats,as.formula)
importFrom(stats,coef)
importFrom(stats,coefficients)
importFrom(stats,confint)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,delete.response)
importFrom(stats,df)
importFrom(stats,df.residual)
importFrom(stats,ecdf)
importFrom(stats,fisher.test)
importFrom(stats,formula)
importFrom(stats,ftable)
importFrom(stats,glm)
importFrom(stats,lm)
importFrom(stats,lm.fit)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,medpolish)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pbeta)
importFrom(stats,pchisq)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,power.t.test)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qf)
importFrom(stats,qt)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,rgeom)
importFrom(stats,rlnorm)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,sigma)
importFrom(stats,terms)
importFrom(stats,uniroot)
importFrom(stats,update)
importFrom(stats,vcov)
importFrom(tibble,add_column)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,tibble)
importFrom(tidyr,nest)
importFrom(tidyr,nesting)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)
importFrom(tidyr,separate_rows)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(utils,unzip)
