API for proBatch
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
| Global functions | |
|---|---|
| add_vertical_batch_borders | Source code |
| adjust_batch_trend_df | Man page Source code |
| adjust_batch_trend_dm | Man page Source code |
| adjust_units | Source code |
| calculate_PVCA | Man page Source code |
| calculate_feature_CV | Man page Source code |
| calculate_peptide_corr_distr | Man page |
| calculate_sample_corr_distr | Man page Source code |
| center_feature_batch_means_df | Man page Source code |
| center_feature_batch_means_dm | Man page Source code |
| center_feature_batch_medians_df | Man page Source code |
| center_feature_batch_medians_dm | Man page Source code |
| check_feature_id_col_in_dm | Source code |
| check_rare_levels | Source code |
| check_sample_consistency | Man page Source code |
| color_list_to_df | Man page |
| correct_batch_effects | Man page |
| correct_batch_effects_df | Man page Source code |
| correct_batch_effects_dm | Man page Source code |
| correct_with_ComBat_df | Man page Source code |
| correct_with_ComBat_dm | Man page Source code |
| create_peptide_annotation | Man page Source code |
| date_to_sample_order | Man page Source code |
| dates_to_posix | Man page Source code |
| define_sample_order | Man page Source code |
| example_peptide_annotation | Man page |
| example_proteome | Man page |
| example_proteome_matrix | Man page |
| example_sample_annotation | Man page |
| feature_level_diagnostics | Man page |
| fit_nonlinear | Man page Source code |
| generate_colors_for_numeric | Man page Source code |
| geom_split_violin | Source code |
| get_sample_corr_df | Source code |
| handle_missing_values | Source code |
| is_batch_factor | Source code |
| loess_regression | Source code |
| loess_regression_opt | Source code |
| log_transform_df | Man page Source code |
| log_transform_dm | Man page Source code |
| long_to_matrix | Man page Source code |
| loocv.nw | Source code |
| map_factors_to_colors | Source code |
| map_numbers_to_colors | Source code |
| matrix_to_long | Man page Source code |
| merge_df_with_annotation | Source code |
| merge_rare_levels | Man page Source code |
| normalize | Man page |
| normalize_data_df | Man page Source code |
| normalize_data_dm | Man page Source code |
| normalize_sample_medians_df | Man page Source code |
| normalize_sample_medians_dm | Man page Source code |
| optimise_bw | Source code |
| optimise_df | Source code |
| plot_CV_distr | Man page Source code |
| plot_CV_distr.df | Man page Source code |
| plot_PCA | Man page Source code |
| plot_PVCA | Man page Source code |
| plot_PVCA.df | Man page Source code |
| plot_boxplot | Man page Source code |
| plot_corr_matrix | Man page Source code |
| plot_heatmap_diagnostic | Man page Source code |
| plot_heatmap_generic | Man page Source code |
| plot_hierarchical_clustering | Man page Source code |
| plot_iRT | Man page Source code |
| plot_peptide_corr_distribution | Man page |
| plot_peptide_corr_distribution.corrDF | Man page |
| plot_peptides_of_one_protein | Man page Source code |
| plot_protein_corrplot | Man page Source code |
| plot_sample_corr_distribution | Man page Source code |
| plot_sample_corr_distribution.corrDF | Man page Source code |
| plot_sample_corr_heatmap | Man page Source code |
| plot_sample_mean | Man page Source code |
| plot_sample_mean_or_boxplot | Man page |
| plot_single_feature | Man page Source code |
| plot_spike_in | Man page Source code |
| plot_split_violin_with_boxplot | Man page Source code |
| plot_with_fitting_curve | Man page Source code |
| prepare_PVCA_df | Man page Source code |
| proBatch | Man page |
| quantile_normalize_df | Man page Source code |
| quantile_normalize_dm | Man page Source code |
| reg.fcn.nw | Source code |
| rle_func | Source code |
| run_ComBat_core | Source code |
| sample_annotation_to_colors | Man page Source code |
| save_ggplot | Source code |
| transform_raw_data | Man page |
| unlog_df | Man page Source code |
| unlog_dm | Man page Source code |
