INTERNAL_FUNCTIONS_BY_FAMILY: Internal Functions by category

In wolski/prolfqua: Proteomics Label Free Quantification

Internal Functions by category

Description

Internal Functions by category

See Also

Other aggregation: aggregate_intensity_topN(), estimate_intensity(), intensity_summary_by_hkeys(), medpolish_estimate(), medpolish_estimate_df(), medpolish_estimate_dfconfig(), medpolish_protein_estimates(), plot_estimate(), plot_hierarchies_add_quantline(), plot_hierarchies_line(), plot_hierarchies_line_df(), rlm_estimate(), rlm_estimate_dfconfig()

Other benchmarking: Benchmark, ionstar_bench_preprocess(), make_benchmark(), ms_bench_add_scores(), ms_bench_auc()

Other configuration: AnalysisConfiguration, AnalysisParameters, AnalysisTableAnnotation, R6_extract_values(), complete_cases(), concrete_AnalysisConfiguration, make_interaction_column(), make_reduced_hierarchy_config(), sample_subset(), separate_factors(), separate_hierarchy(), setup_analysis(), spread_response_by_IsotopeLabel(), table_factors(), table_factors_size()

Other deprecated: intensity_summary_by_hkeys(), medpolish_protein_estimates()

Other modelling: Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, LR_test(), Model, build_model(), contrasts_fisher_exact(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), isSingular_lm(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_limma(), moderated_p_limma_long(), my_contest(), my_contrast(), my_contrast_V1(), my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_predictions(), sim_build_models_lm(), sim_build_models_lmer(), sim_make_model_lm(), sim_make_model_lmer(), strategy_lmer(), summary_ROPECA_median_p.scaled()

Other plotting: ContrastsPlotter, UpSet_interaction_missing_stats(), UpSet_missing_stats(), medpolish_estimate_df(), missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_NA_heatmap(), plot_estimate(), plot_heatmap(), plot_heatmap_cor(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line(), plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_pca(), plot_raster(), plot_sample_correlation(), plot_screeplot()

Other preprocessing: apply_to_response_matrix(), filter_proteins_by_peptide_count(), get_robscales(), normalize_log2_robscale(), robust_scale(), scale_with_subset(), scale_with_subset_by_factors()

Other stats: lfq_power_t_test_proteins(), lfq_power_t_test_quantiles(), lfq_power_t_test_quantiles_V2(), plot_stat_density(), plot_stat_density_median(), plot_stat_violin(), plot_stat_violin_median(), plot_stdv_vs_mean(), pooled_V2(), summarize_stats()

Other summary: hierarchy_counts(), hierarchy_counts_sample(), nr_B_in_A_per_sample(), summarize_hierarchy()

Other utilities: get_UniprotID_from_fasta_header(), matrix_to_tibble(), multigroup_volcano(), names_to_matrix(), pairs_smooth(), pairs_w_abline(), panel_cor(), panel_hist(), remove_NA_rows(), table_facade()

Other vignetteHelpers: render_MQSummary_rmd()

wolski/prolfqua documentation built on Dec. 4, 2024, 11:18 p.m.