Internal Functions by category
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()
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()