Internal Functions by category
See also
Other aggregation:
aggregate_intensity_topN(),
estimate_intensity(),
medpolish_estimate(),
medpolish_estimate_df(),
medpolish_estimate_dfconfig(),
plot_estimate(),
plot_hierarchies_add_quantline(),
plot_hierarchies_line(),
plot_hierarchies_line_df(),
rlm_estimate(),
rlm_estimate_dfconfig()
Other configuration:
AnalysisConfiguration,
R6_extract_values(),
complete_cases(),
make_interaction_column(),
make_reduced_hierarchy_config(),
sample_subset(),
separate_hierarchy(),
setup_analysis(),
table_factors(),
table_factors_size()
Other modelling:
AnovaExtractor,
Contrasts,
ContrastsDEqMSFacade,
ContrastsDEqMSVoomFacade,
ContrastsFirth,
ContrastsFirthFacade,
ContrastsLMFacade,
ContrastsLMImputeFacade,
ContrastsLMMissingFacade,
ContrastsLimma,
ContrastsLimmaFacade,
ContrastsLimmaImputeFacade,
ContrastsLimmaVoomFacade,
ContrastsLimmaVoomImputeFacade,
ContrastsLimpaFacade,
ContrastsLmerFacade,
ContrastsMissing,
ContrastsModerated,
ContrastsModeratedDEqMS,
ContrastsPlotter,
ContrastsRLMFacade,
ContrastsROPECA,
ContrastsROPECAFacade,
ContrastsTable,
LR_test(),
Model,
ModelFirth,
ModelLimma,
StrategyLM,
StrategyLimma,
StrategyLimpa,
StrategyLmer,
StrategyLogistf,
StrategyRLM,
build_contrast_analysis(),
build_model(),
build_model_glm_peptide(),
build_model_glm_protein(),
build_model_impute(),
build_model_limma(),
build_model_limma_impute(),
build_model_limma_voom(),
build_model_limma_voom_impute(),
build_model_limpa(),
build_model_logistf(),
compute_borrowed_variance(),
compute_borrowed_variance_limma(),
compute_contrast(),
compute_lmer_contrast(),
contrasts_fisher_exact(),
get_anova_df(),
get_complete_model_fit(),
get_p_values_pbeta(),
group_label(),
impute_refit_singular(),
isSingular_lm(),
linfct_all_possible_contrasts(),
linfct_factors_contrasts(),
linfct_from_model(),
linfct_matrix_contrasts(),
merge_contrasts_results(),
model_analyse(),
model_summary(),
moderated_p_deqms(),
moderated_p_deqms_long(),
moderated_p_limma(),
moderated_p_limma_long(),
new_lm_imputed(),
pivot_model_contrasts_2_Wide(),
plot_lmer_peptide_predictions(),
sim_build_models_lm(),
sim_build_models_lmer(),
sim_build_models_logistf(),
sim_make_model_lm(),
sim_make_model_lmer(),
strategy_limma(),
strategy_limpa(),
strategy_logistf(),
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()
Other preprocessing:
apply_to_response_matrix(),
filter_proteins_by_peptide_count(),
get_robscales(),
robust_scale(),
scale_with_subset()
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:
HierarchyCountsSample,
hierarchy_counts(),
hierarchy_counts_sample(),
summarize_hierarchy()
Other utilities:
get_UniprotID_from_fasta_header(),
matrix_to_tibble(),
multigroup_volcano(),
names_to_matrix(),
pairs_smooth(),
panel_cor(),
remove_NA_rows(),
table_facade()