Files in wolski/prolfqua

Proteomics Label Free Quantification

.github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/custom.md .github/ISSUE_TEMPLATE/feature_request.md CODE_OF_CONDUCT.md LICENSE.md R/A_dataset_docu.R R/AnalysisConfiguration.R R/AnalysisParameters.R R/AnalysisTableAnnotation.R R/Benchmark.R R/Contrasts.R R/ContrastsInterface.R R/ContrastsModerated.R R/ContrastsPlotter.R R/ContrastsProDA.R R/ContrastsROPECA.R R/ContrastsSimpleImpute.R R/ContrastsTable.R R/LFQData.R R/LFQDataAggregator.R R/LFQDataPlotter.R R/LFQDataStats.R R/LFQDataSummariser.R R/LFQDataTransformer.R R/LFQDataWriter.R R/Model.R R/ModelInterface.R R/simulate_LFQ_data.R R/squeezeVarRob.R R/tidyMS_MQ_workflow.R R/tidyMS_R6Model.R R/tidyMS_R6_ConcreteConfigurations.R R/tidyMS_R6_Modelling.R R/tidyMS_R6_TransitionCorrelations.R R/tidyMS_aggregation.R R/tidyMS_missigness.R R/tidyMS_missigness_V2.R R/tidyMS_plotting.R R/tidyMS_stats.R R/tidyMS_write.R R/utilities.R R/vignetteHelpers.R README.md inst/deprecated/DEPRECATED.R inst/issue71/prolfqua_contrast_testCode.R man/AnalysisConfiguration.Rd man/AnalysisParameters.Rd man/AnalysisTableAnnotation.Rd man/Benchmark.Rd man/Contrasts.Rd man/ContrastsInterface.Rd man/ContrastsMissing.Rd man/ContrastsModerated.Rd man/ContrastsPlotter.Rd man/ContrastsProDA.Rd man/ContrastsROPECA.Rd man/ContrastsTable.Rd man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd man/LFQData.Rd man/LFQDataAggregator.Rd man/LFQDataPlotter.Rd man/LFQDataStats.Rd man/LFQDataSummariser.Rd man/LFQDataToSummarizedExperiment.Rd man/LFQDataTransformer.Rd man/LFQDataWriter.Rd man/LR_test.Rd man/MissingHelpers.Rd man/Model.Rd man/ModelInterface.Rd man/PACKAGE_DATA.Rd man/R6_extract_values.Rd man/UpSet_interaction_missing_stats.Rd man/UpSet_missing_stats.Rd man/adjust_p_values.Rd man/aggregate_intensity_topN.Rd man/apply_to_response_matrix.Rd man/build_model.Rd man/complete_cases.Rd man/concrete_AnalysisConfiguration.Rd man/contrasts_fisher_exact.Rd man/contrasts_linfct.Rd man/cor_jackknife_matrix.Rd man/cor_order.Rd man/data_IonstarProtein_subsetNorm.Rd man/data_SAINTe_output.Rd man/data_benchmarkExample.Rd man/data_checksummarizationrobust87.Rd man/data_checksummarizerobust.Rd man/data_checksummarizerobust69.Rd man/data_correlatedPeptideList.Rd man/data_ionstar.Rd man/data_skylinePRMSample_A.Rd man/data_skylineSRM_HL_A.Rd man/data_spectronautDIA250_A.Rd man/data_test_confusion_matrix_scores.Rd man/dot-get_robscales.Rd man/dot-summarise_missing_contrasts.Rd man/estimate_intensity.Rd man/filter_byQValue.Rd man/filter_difference.Rd man/filter_proteins_by_peptide_count.Rd man/find_package_file.Rd man/get_UniprotID_from_fasta_header.Rd man/get_anova_df.Rd man/get_complete_model_fit.Rd man/get_contrast.Rd man/get_p_values_pbeta.Rd man/get_robscales.Rd man/hierarchy_counts.Rd man/hierarchy_counts_sample.Rd man/intensity_summary_by_hkeys.Rd man/interaction_missing_stats.Rd man/ionstar_bench_preprocess.Rd man/isSingular_lm.Rd man/jackknife.Rd man/jackknife_matrix.Rd man/lfq_power_t_test_proteins.Rd man/lfq_power_t_test_quantiles.Rd man/lfq_power_t_test_quantiles_V2.Rd man/lfq_write_table.Rd man/linfct_all_possible_contrasts.Rd man/linfct_factors_contrasts.Rd man/linfct_from_model.Rd man/linfct_matrix_contrasts.Rd man/make_benchmark.Rd man/make_interaction_column.Rd man/make_reduced_hierarchy_config.Rd man/matrix_to_tibble.Rd man/medpolish_estimate.Rd man/medpolish_estimate_df.Rd man/medpolish_estimate_dfconfig.Rd man/medpolish_protein_estimates.Rd man/merge_contrasts_results.Rd man/missigness_histogram.Rd man/missingness_per_condition.Rd man/missingness_per_condition_cumsum.Rd man/model_analyse.Rd man/model_summary.Rd man/moderated_p_limma.Rd man/moderated_p_limma_long.Rd man/ms_bench_add_scores.Rd man/ms_bench_auc.Rd man/multigroup_volcano.Rd man/my_contest.Rd man/my_contrast.Rd man/my_contrast_V1.Rd man/my_contrast_V2.Rd man/my_glht.Rd man/names_to_matrix.Rd man/normalize_log2_robscale.Rd man/nr_B_in_A.Rd man/nr_B_in_A_per_sample.Rd man/nr_obs_experiment.Rd man/nr_obs_sample.Rd man/old2new.Rd man/pairs_smooth.Rd man/pairs_w_abline.Rd man/panel_cor.Rd man/panel_hist.Rd man/pivot_model_contrasts_2_Wide.Rd man/plot_NA_heatmap.Rd man/plot_estimate.Rd man/plot_heatmap.Rd man/plot_heatmap_cor.Rd man/plot_hierarchies_add_quantline.Rd man/plot_hierarchies_boxplot.Rd man/plot_hierarchies_boxplot_df.Rd man/plot_hierarchies_line.Rd man/plot_hierarchies_line_df.Rd man/plot_intensity_distribution_violin.Rd man/plot_lmer_peptide_predictions.Rd man/plot_pca.Rd man/plot_raster.Rd man/plot_sample_correlation.Rd man/plot_screeplot.Rd man/plot_stat_density.Rd man/plot_stat_density_median.Rd man/plot_stat_violin.Rd man/plot_stat_violin_median.Rd man/plot_stdv_vs_mean.Rd man/pooled_var.Rd man/prolfqua_data.Rd man/rank_by_NA.Rd man/rank_peptide_by_intensity.Rd man/remove_NA_rows.Rd man/remove_large_QValues.Rd man/remove_small_intensities.Rd man/render_MQSummary_rmd.Rd man/response_as_matrix.Rd man/response_matrix_as_tibble.Rd man/rlm_estimate.Rd man/rlm_estimate_dfconfig.Rd man/robust_scale.Rd man/sample_subset.Rd man/scale_with_subset.Rd man/scale_with_subset_by_factors.Rd man/scriptCopyHelperVec.Rd man/separate_factors.Rd man/separate_hierarchy.Rd man/setup_analysis.Rd man/sim_build_models_lm.Rd man/sim_build_models_lmer.Rd man/sim_lfq_data.Rd man/sim_lfq_data_2Factor_config.Rd man/sim_lfq_data_peptide_config.Rd man/sim_lfq_data_protein_config.Rd man/sim_make_model_lm.Rd man/sim_make_model_lmer.Rd man/spread_response_by_IsotopeLabel.Rd man/squeezeVarRob.Rd man/strategy.Rd man/summarise_QValues.Rd man/summarize_hierarchy.Rd man/summarize_stats.Rd man/summarize_stats_factors.Rd man/summary_ROPECA_median_p.scaled.Rd man/table_facade.Rd man/table_factors.Rd man/table_factors_size.Rd man/tidy_to_wide.Rd man/tidy_to_wide_config.Rd man/transform_work_intensity.Rd man/volcano_Plotly.Rd man/which_missing.Rd tests/testthat.R tests/testthat/cleanup.R tests/testthat/test-plotting_functions.R tests/testthat/test-tidyconfig_functions.R vignettes/Comparing2Groups.Rmd vignettes/CreatingConfigurations.Rmd vignettes/Modelling2Factors.Rmd vignettes/QCandSampleSize.Rmd vignettes/QualityControlAndSampleSizeEstimation.Rmd vignettes/SimulateData.Rmd vignettes/TestingMissingInference.Rmd