API for wolski/prolfqua
Proteomics Label Free Quantification
| Global functions | |
|---|---|
| .ExtractMatrix | Source code |
| .coeff_weights_factor_levels | Source code |
| .ehandler | Source code Source code |
| .extractInt | Source code |
| .generate_random_string | Source code |
| .get_match_idx | Source code |
| .get_robscales | Man page Source code |
| .get_sides | Source code |
| .lfq_power_t_test_quantiles | Source code |
| .likelihood_ratio_test | Source code |
| .linfct | Source code |
| .lmer4_coeff_matrix | Source code |
| .make_name_AinB | Source code |
| .multigroup_volcano | Source code |
| .nr_B_in_A | Source code |
| .partial_AUC_summary | Source code |
| .plot_ROC | Source code |
| .plot_precision_recall | Source code |
| .plot_score_distribution | Source code |
| .rankProteinPrecursors | Source code |
| .reestablish_condition | Source code |
| .rlm_estimate | Source code |
| .run_markdown_with_params | Source code |
| .scale_probabilities | Source code |
| .squeezeVarRob | Source code |
| .summarise_missing_contrasts | Man page Source code |
| AnalysisConfiguration | Man page |
| AnalysisParameters | Man page |
| AnalysisTableAnnotation | Man page |
| Benchmark | Man page |
| Contrasts | Man page |
| ContrastsInterface | Man page |
| ContrastsMissing | Man page |
| ContrastsModerated | Man page |
| ContrastsPlotter | Man page |
| ContrastsProDA | Man page |
| ContrastsROPECA | Man page |
| ContrastsTable | Man page |
| INTERNAL_FUNCTIONS_BY_FAMILY | Man page |
| LFQData | Man page |
| LFQDataAggregator | Man page |
| LFQDataPlotter | Man page |
| LFQDataStats | Man page |
| LFQDataSummariser | Man page |
| LFQDataToSummarizedExperiment | Man page Source code |
| LFQDataTransformer | Man page |
| LFQDataWriter | Man page |
| LR_test | Man page Source code |
| MissingHelpers | Man page |
| Model | Man page |
| ModelInterface | Man page |
| PACKAGE_DATA | Man page |
| R6_extract_values | Man page Source code |
| UpSet_interaction_missing_stats | Man page Source code |
| UpSet_missing_stats | Man page Source code |
| adjust_p_values | Man page Source code |
| aggregate_intensity_topN | Man page Source code |
| apply_to_response_matrix | Man page Source code |
| build_model | Man page Source code |
| complete_cases | Man page Source code |
| compute_pooled | Man page Source code |
| concrete_AnalysisConfiguration | Man page |
| contrasts_fisher_exact | Man page Source code |
| contrasts_linfct | Man page Source code |
| cor_jackknife_matrix | Man page Source code |
| cor_order | Man page Source code |
| create_config_MQ_peptide | Man page Source code |
| create_config_MSFragger_MSstats | Man page Source code |
| create_config_Skyline | Man page Source code |
| create_config_Spectronaut_Peptide | Man page Source code |
| data_IonstarProtein_subsetNorm | Man page |
| data_SAINTe_output | Man page |
| data_benchmarkExample | Man page |
| data_checksummarizationrobust87 | Man page |
| data_checksummarizerobust | Man page |
| data_checksummarizerobust69 | Man page |
| data_correlatedPeptideList | Man page |
| data_ionstar | Man page |
| data_skylinePRMSample_A | Man page |
| data_skylineSRM_HL_A | Man page |
| data_spectronautDIA250_A | Man page |
| data_test_confusion_matrix_scores | Man page |
| do_confusion | Source code |
| do_confusion_c | Source code |
| estimate_intensity | Man page Source code |
| filter_byQValue | Man page Source code |
| filter_difference | Man page Source code |
| filter_proteins_by_peptide_count | Man page Source code |
| find_package_file | Man page Source code |
| fitFDistRobustly_LG | Source code |
| fitFDist_LG | Source code |
| get_UniprotID_from_fasta_header | Man page Source code |
| get_anova_df | Man page Source code |
| get_complete_model_fit | Man page Source code |
| get_contrast | Man page Source code |
| get_p_values_pbeta | Man page Source code |
| get_robscales | Man page Source code |
| hierarchy_counts | Man page Source code |
| hierarchy_counts_sample | Man page Source code |
| intensity_summary_by_hkeys | Man page Source code |
| interaction_missing_stats | Man page Source code |
| ionstar_bench_preprocess | Man page Source code |
| isSingular_lm | Man page Source code |
| jackknife | Man page Source code |
| jackknife_matrix | Man page Source code |
| lfq_power_t_test_proteins | Man page Source code |
| lfq_power_t_test_quantiles | Man page Source code |
| lfq_power_t_test_quantiles_V2 | Man page Source code |
| lfq_write_table | Man page Source code |
| linfct_all_possible_contrasts | Man page Source code |
| linfct_factors_contrasts | Man page Source code |
| linfct_from_model | Man page Source code |
| linfct_matrix_contrasts | Man page Source code |
| make_benchmark | Man page Source code |
| make_interaction_column | Man page Source code |
| make_reduced_hierarchy_config | Man page Source code |
| matrix_to_tibble | Man page Source code |
| medpolish_estimate | Man page Source code |
| medpolish_estimate_df | Man page Source code |
| medpolish_estimate_dfconfig | Man page Source code |
| medpolish_protein_estimates | Man page Source code |
| merge_contrasts_results | Man page Source code |
| missigness_histogram | Man page Source code |
| missingness_per_condition | Man page Source code |
| missingness_per_condition_cumsum | Man page Source code |
| model_analyse | Man page Source code |
| model_summary | Man page Source code |
| moderated_p_limma | Man page Source code |
| moderated_p_limma_long | Man page Source code |
| ms_bench_add_scores | Man page Source code |
| ms_bench_auc | Man page Source code |
| multigroup_volcano | Man page Source code |
| my_contest | Man page Source code |
| my_contrast | Man page Source code |
| my_contrast_V1 | Man page Source code |
| my_contrast_V2 | Man page Source code |
| my_glht | Man page Source code |
| names_to_matrix | Man page Source code |
| normalize_log2_robscale | Man page Source code |
| nr_B_in_A | Man page Source code |
| nr_B_in_A_per_sample | Man page Source code |
| nr_obs_experiment | Man page Source code |
| nr_obs_sample | Man page Source code |
| old2new | Man page Source code |
| pairs_smooth | Man page |
| pairs_w_abline | Man page Source code |
| panel_cor | Man page Source code |
| panel_hist | Man page Source code |
| pivot_model_contrasts_2_Wide | Man page Source code |
| plot_NA_heatmap | Man page Source code |
| plot_estimate | Man page Source code |
| plot_heatmap | Man page Source code |
| plot_heatmap_cor | Man page Source code |
| plot_hierarchies_add_quantline | Man page Source code |
| plot_hierarchies_boxplot | Man page Source code |
| plot_hierarchies_boxplot_df | Man page Source code |
| plot_hierarchies_line | Man page Source code |
| plot_hierarchies_line_default | Source code |
| plot_hierarchies_line_df | Man page Source code |
| plot_intensity_distribution_density | Man page Source code |
| plot_intensity_distribution_violin | Man page Source code |
| plot_lmer_peptide_predictions | Man page Source code |
| plot_pca | Man page Source code |
| plot_raster | Man page Source code |
| plot_sample_correlation | Man page Source code |
| plot_screeplot | Man page Source code |
| plot_stat_density | Man page Source code |
| plot_stat_density_median | Man page Source code |
| plot_stat_violin | Man page Source code |
| plot_stat_violin_median | Man page Source code |
| plot_stdv_vs_mean | Man page Source code |
| pooled_V1 | Man page Source code |
| pooled_V2 | Man page Source code |
| poolvar | Man page Source code |
| prolfqua_data | Man page |
| rank_by_NA | Man page Source code |
| rank_peptide_by_intensity | Man page Source code |
| remove_NA_rows | Man page Source code |
| remove_large_QValues | Man page Source code |
| remove_small_intensities | Man page Source code |
| render_MQSummary_rmd | Man page Source code |
| response_as_matrix | Man page Source code |
| response_matrix_as_tibble | Man page Source code |
| rlm_estimate | Man page Source code |
| rlm_estimate_dfconfig | Man page Source code |
| robust_scale | Man page Source code |
| sample_subset | Man page Source code |
| scale_with_subset | Man page Source code |
| scale_with_subset_by_factors | Man page Source code |
| scriptCopyHelperVec | Man page Source code |
| separate_factors | Man page Source code |
| separate_hierarchy | Man page Source code |
| setup_analysis | Man page Source code |
| sim_build_models_lm | Man page Source code |
| sim_build_models_lmer | Man page Source code |
| sim_lfq_data | Man page Source code |
| sim_lfq_data_2Factor_config | Man page Source code |
| sim_lfq_data_peptide_config | Man page Source code |
| sim_lfq_data_protein_config | Man page Source code |
| sim_make_model_lm | Man page Source code |
| sim_make_model_lmer | Man page Source code |
| spread_response_by_IsotopeLabel | Man page Source code |
| squeezeVarRob | Man page Source code |
| strategy_glm | Man page Source code |
| strategy_lm | Man page Source code |
| strategy_lmer | Man page Source code |
| strategy_rlm | Man page Source code |
| summarise_QValues | Man page Source code |
| summarize_hierarchy | Man page Source code |
| summarize_stats | Man page Source code |
| summarize_stats_all | Man page Source code |
| summarize_stats_factors | Man page Source code |
| summarize_stats_quantiles | Man page Source code |
| summary_ROPECA_median_p.scaled | Man page Source code |
| table_facade | Man page |
| table_factors | Man page Source code Source code |
| table_factors_size | Man page Source code |
| tidy_to_wide | Man page Source code |
| tidy_to_wide_config | Man page Source code |
| transform_work_intensity | Man page Source code |
| upper.panel | Source code |
| volcano_plotly | Man page |
| which_missing | Man page Source code |
