Man pages for metasnf
Meta Clustering with Similarity Network Fusion
| abcd_anxiety | Mock ABCD anxiety data |
| abcd_colour | Mock ABCD "colour" data |
| abcd_cort_sa | Mock ABCD cortical surface area data |
| abcd_cort_t | Mock ABCD cortical thickness data |
| abcd_depress | Mock ABCD depression data |
| abcd_h_income | Mock ABCD income data |
| abcd_income | Mock ABCD income data |
| abcd_pubertal | Mock ABCD pubertal status data |
| abcd_subc_v | Mock ABCD subcortical volumes data |
| add_columns | Add columns to a data frame |
| add_settings_df_rows | Add rows to a settings_df |
| adjusted_rand_index_heatmap | Heatmap of pairwise adjusted rand indices between solutions |
| age_df | Mock age data |
| alluvial_cluster_plot | Alluvial plot of patients across cluster counts and important... |
| anxiety | Mock ABCD anxiety data |
| arrange_dll | Sort data frames in a data list by their unique ID values |
| as_ari_matrix | Convert an object to an ARI matrix |
| as.data.frame.data_list | Coerce a 'data_list' class object into a 'data.frame' class... |
| as.data.frame.ext_solutions_df | Coerce a 'ext_solutions_df' class object into a 'data.frame'... |
| as.data.frame.settings_df | Coerce a 'settings_df' class object into a 'data.frame' class... |
| as.data.frame.snf_config | Coerce a 'settings_df' class object into a 'data.frame' class... |
| as.data.frame.solutions_df | Coerce a 'solutions_df' class object into a 'data.frame'... |
| as.data.frame.t_ext_solutions_df | Coerce a 't_ext_solutions_df' class object into a... |
| as.data.frame.t_solutions_df | Coerce a 't_solutions_df' class object into a 'data.frame'... |
| as.data.frame.weights_matrix | Coerce a 'weights_matrix' class object into a 'data.frame'... |
| as_data_list | Convert an object to a data list |
| as.list.clust_fns_list | Coerce a 'clust_fns_list' class object into a 'list' class... |
| as.list.data_list | Coerce a 'data_list' class object into a 'list' class object |
| as.list.dist_fns_list | Coerce a 'dist_fns_list' class object into a 'list' class... |
| as.list.sim_mats_list | Coerce a 'sim_mats_list' class object into a 'list' class... |
| as.list.snf_config | Coerce a 'snf_config' class object into a 'list' class object |
| as.matrix.ari_matrix | Coerce a 'ari_matrix' class object into a 'matrix' class... |
| as.matrix.weights_matrix | Coerce a 'weights_matrix' class object into a 'matrix' class... |
| assemble_data | Collapse a data frame and/or a data list into a single data... |
| as_settings_df | Convert an object to a settings data frame |
| as_sim_mats_list | Convert an object to a similarity matrix list |
| as_snf_config | Convert an object to a snf config |
| assoc_pval_heatmap | Heatmap of pairwise associations between features |
| as_weights_matrix | Convert an object to a weights matrix |
| auto_plot | Automatically plot features across clusters |
| bar_plot | Bar plot separating a feature by cluster |
| batch_row_closure | Generate closure function to run batch_snf in an... |
| batch_snf | Run variations of SNF |
| batch_snf_subsamples | Run SNF clustering pipeline on a list of subsampled data... |
| cache_a_complete_example_ext_sol_df | Cached example extended solutions data frame |
| cache_a_complete_example_lp_ext_sol_df | Cached example extended solutions data frame |
| cache_a_complete_example_sol_df | Cached example solutions data frame |
| calc_aris | Construct an ARI matrix storing inter-solution similarities |
| calc_assoc_pval | Calculate p-values based on feature vectors and their types |
| calc_assoc_pval_matrix | Calculate p-values for all pairwise associations of features... |
| calc_nmis | Calculate feature NMIs for a data list and a solutions data... |
| calculate_coclustering | Calculate co-clustering data |
| cancer_diagnosis_df | Mock diagnosis data |
| cat_colours | Helper function for generating categorical colour palette |
| cell_significance_fn | Place significance stars on ComplexHeatmap cells |
| char_to_fac | Convert character-type columns of a data frame to factor-type |
| check_cfll_fn_args | Check if functions in a distance metrics list-like have valid... |
| check_cfll_fns | Check if items of a clustering functions list-like object are... |
| check_cfll_named | Check if clustering functions list-like object has named... |
| check_cfll_unique_names | Check if names in a clustering functions list-like object are... |
| check_compatible_sdf_cfl | Check if settings_df exceeds bounds of clust_fns_list |
| check_compatible_sdf_dfl | Check if settings_df exceeds bounds of dist_fns_list |
| check_compatible_sdf_wm | Check if settings_df and weights_matrix have same number of... |
| check_dataless_annotations | Helper function to stop annotation building when no data was... |
| check_dfll_fn_args | Check if functions in a distance metrics list-like have valid... |
| check_dfll_fn_names | Check if functions in a distance metrics list-like have names |
| check_dfll_item_names | Check if items of a distance metrics list-like object have... |
| check_dfll_subitems_are_fns | Check if items of a distance metrics list-like object are... |
| check_dfll_unique_names | Check if names in a distance metrics list-like object are... |
| check_dll_duplicate_components | Check if data list contains any duplicate names |
| check_dll_duplicate_features | Check if data list contains any duplicate features |
| check_dll_empty_input | Error if empty input provided during data list initialization |
| check_dll_four_subitems | Error if data list-like list doesn't have only 4-item nested... |
| check_dll_inherits_list | Error if data list-like structure isn't a list |
| check_dll_subitem_classes | Check if UID columns in a nested list have valid structure... |
| check_dll_subitem_names | Check valid item names for a data list-like list |
| check_dll_types | Error if data list-like structure has invalid feature types |
| check_dll_uid | Check if UID columns in a nested list have valid structure... |
| check_hm_dependencies | Check for ComplexHeatmap and circlize dependencies |
| check_sdfl_colnames | Check if settings data frame inherits class 'data.frame' |
| check_sdfl_is_df | Check if settings data frame inherits class 'data.frame' |
| check_sdfl_numeric | Check if settings data frame is numeric |
| check_similarity_matrices | Check validity of similarity matrices |
| check_valid_k | Check if max K exceeds the number of observations |
| check_valid_sc | Check if SNF config has valid structure |
| chi_squared_pval | Chi-squared test p-value (generic) |
| clust_fns | Built-in clustering algorithms |
| clust_fns_list | Build a clustering algorithms list |
| cocluster_density | Density plot of co-clustering stability across subsampled... |
| cocluster_heatmap | Heatmap of observation co-clustering across resampled data |
| coclustering_coverage_check | Co-clustering coverage check |
| collapse_dl | Convert a data list into a data frame |
| colour_scale | Return a colour ramp for a given vector |
| convert_uids | Convert unique identifiers of data list to "uid" |
| cort_sa | Mock ABCD cortical surface area data |
| cort_t | Mock ABCD cortical thickness data |
| data_list | Build a 'data_list' class object |
| depress | Mock ABCD depression data |
| diagnosis_df | Mock diagnosis data |
| discretisation | Internal function for 'estimate_nclust_given_graph' |
| discretisation_evec_data | Internal function for 'estimate_nclust_given_graph' |
| dist_fns | Built-in distance functions |
| dist_fns_list | Build a distance metrics list |
| dlapply | Apply-like function for data list objects |
| dll_uid_first_col | Make the uid UID columns of a data list first |
| dl_variable_summary | Variable-level summary of a data list |
| domains | Pull domains from a data list |
| dplyr_row_slice.ext_solutions_df | Function to extend dplyr to extended solutions data frame... |
| dplyr_row_slice.solutions_df | Function to extend dplyr to solutions data frame objects |
| drop_cols | Helper function to remove columns from a data frame |
| drop_inputs | Execute inclusion |
| ensure_dll_df | Ensure the data item of each component is a 'data.frame'... |
| esm_manhattan_plot | Manhattan plot of feature-cluster association p-values |
| estimate_nclust_given_graph | Estimate number of clusters for a similarity matrix |
| expression_df | Modification of SNFtool mock data frame "Data1" |
| extend_solutions | Extend a solutions data frame to include outcome evaluations |
| ext_solutions_df | Constructor for 'ext_solutions_df' class object |
| fav_colour | Mock ABCD "colour" data |
| features | Return character vector of features stored in an object |
| fisher_exact_pval | Fisher exact test p-value |
| gender_df | Mock gender data |
| generate_annotations_list | Generate annotations list |
| generate_clust_algs_list | Generate a clustering algorithms list |
| generate_distance_metrics_list | Generate a list of distance metrics |
| generate_settings_matrix | Build a settings data frame |
| get_cluster_df | Extract cluster membership information from one solutions... |
| get_clusters | Extract cluster membership vector from one solutions data... |
| get_cluster_solutions | Extract cluster membership information from a sol_df |
| get_complete_uids | Pull complete-data UIDs from a list of data frames |
| get_dist_matrix | Calculate distance matrices |
| get_dl_uids | Extract UIDs from a data list |
| get_heatmap_order | Return the row or column ordering present in a heatmap |
| get_matrix_order | Return the hierarchical clustering order of a matrix |
| get_mean_pval | Get mean p-value |
| get_min_pval | Get minimum p-value |
| get_pvals | Get p-values from an extended solutions data frame |
| get_representative_solutions | Extract representative solutions from a matrix of ARIs |
| gexclude | Helper function to drop columns from a data frame by grepl... |
| gselect | Helper function to pick columns from a data frame by 'grepl'... |
| income | Mock ABCD income data |
| is_data_list | Test if the object is a data list |
| jitter_plot | Jitter plot separating a feature by cluster |
| label_meta_clusters | Assign meta cluster labels to rows of a solutions data frame... |
| label_prop | Label propagation |
| label_propagate | Label propagate cluster solutions to non-clustered... |
| label_splits | Convert a vector of partition indices into meta cluster... |
| linear_adjust | Linearly correct data list by features with unwanted signal |
| linear_model_pval | Linear model p-value (generic) |
| mc_manhattan_plot | Manhattan plot of feature-meta cluster association p-values |
| merge.clust_fns_list | Merge 'clust_fns_list' objects |
| merge.data_list | Merge observations between two compatible data lists |
| merge_df_list | Merge list of data frames into a single data frame |
| merge.dist_fns_list | Merge 'dist_fns_list' objects |
| merge.ext_solutions_df | Merge 'ext_solutions_df' objects |
| merge.settings_df | Merge 'settings_df' objects |
| merge.sim_mats_list | Merge 'sim_mats_list' objects |
| merge.snf_config | Merge method for SNF config objects |
| merge.solutions_df | Merge 'solutions_df' objects |
| merge.t_ext_solutions_df | Merge 't_ext_solutions_df' objects |
| merge.t_solutions_df | Merge 't_solutions_df' objects |
| merge.weights_matrix | Merge 'weights_matrix' objects |
| metasnf_alert | Helper function for raising alerts |
| metasnf_defunct | Helper function for defunct function errors |
| metasnf_deprecated | Helper function for deprecated function warnings |
| metasnf_error | Helper function for raising errors |
| metasnf-package | metasnf: Meta Clustering with Similarity Network Fusion |
| metasnf_warning | Helper function for raising warnings |
| methylation_df | Modification of SNFtool mock data frame "Data2" |
| mock_ari_matrix | Mock example of an 'ari_matrix' metasnf object |
| mock_clust_fns_list | Mock example of a 'clust_fns_list' metasnf object |
| mock_data_list | Mock example of a 'data_list' metasnf object |
| mock_dist_fns_list | Mock example of a 'dist_fns_list' metasnf object |
| mock_ext_solutions_df | Mock example of a 'ext_solutions_df' metasnf object |
| mock_mc_solutions_df | Mock example of a 'mc_solutions_df' metasnf object |
| mock_rep_solutions_df | Mock example of a 'rep_solutions_df' metasnf object |
| mock_settings_df | Mock example of a 'settings_df' metasnf object |
| mock_snf_config | Mock example of a 'snf_config' metasnf object |
| mock_solutions_df | Mock example of a 'solutions_df' metasnf object |
| mock_t_solutions_df | Mock example of a 't_solutions_df' metasnf object |
| mock_weights_matrix | Mock example of a 'weights_matrix' metasnf object |
| new_ari_matrix | Constructor for 'ari_matrix' class object |
| new_clust_fns_list | Constructor for 'clust_fns_list' class object |
| new_data_list | Constructor for 'data_list' class object |
| new_dist_fns_list | Constructor for 'dist_fns_list' class object |
| new_ext_solutions_df | Constructor for 'ext_solutions_df' class object |
| new_settings_df | Constructor for 'settings_df' class object |
| new_sim_mats_list | Constructor for 'similarity_matrix_list' class object |
| new_snf_config | Constructor for 'snf_config' class object |
| new_solutions_df | Constructor for 'solutions_df' class object |
| new_weights_matrix | Constructor for 'weights_matrix' class object |
| n_features | Extract number of features stored in an object |
| n_observations | Extract number of observations stored in an object |
| not_shown_message | Helper function for creating what hidden ft/obs/sols message |
| numcol_to_numeric | Convert columns of a data frame to numeric type (if possible) |
| ord_reg_pval | Ordinal regression p-value |
| parallel_batch_snf | Parallel processing form of batch_snf |
| pick_cols | Helper function to pick columns from a data frame |
| pl | Helper function to pluralize a string |
| plot.ari_matrix | Heatmap of pairwise adjusted rand indices between solutions |
| plot.data_list | Plot of feature values in a data list |
| plot.ext_solutions_df | Plot of cluster assignments in an extended solutions data... |
| plot.snf_config | Heatmap for visualizing an SNF config |
| plot.solutions_df | Plot of cluster assignments in a solutions data frame |
| prefix_dll_uid | Add "uid_" prefix to all UID values in uid column |
| print.ari_matrix | Print method for class 'ari_matrix' |
| print.clust_fns_list | Print method for class 'clust_fns_list' |
| print.data_list | Print method for class 'data_list' |
| print.dist_fns_list | Print method for class 'dist_fns_list' |
| print.ext_solutions_df | Print method for class 'ext_solutions_df' |
| print.settings_df | Print method for class 'settings_df' |
| print.sim_mats_list | Print method for class 'sim_mats_list' |
| print.snf_config | Print method for class 'snf_config' |
| print.solutions_df | Print method for class 'solutions_df' |
| print.t_ext_solutions_df | Print method for class 't_ext_solutions_df' |
| print.t_solutions_df | Print method for class 't_solutions_df' |
| print.weights_matrix | Print method for class 'weights_matrix' |
| print_with_n_message | Helper function for outputting tip on changing rows printed |
| print_with_t_message | Helper function for transposing solutions_df message |
| pubertal | Mock ABCD pubertal status data |
| pval_heatmap | Heatmap of p-values |
| quality_measures | Quality metrics |
| random_removal | Generate random removal sequence |
| rbind.ext_solutions_df | Row-binding of solutions data frame class objects |
| rbind.solutions_df | Row-binding of solutions data frame class objects |
| rbind.t_solutions_df | Row-binding of t_solutions_df class objects |
| rbind.weights_matrix | Row-bind weights matrices |
| remove_dll_incomplete | Remove observations with incomplete data from a data... |
| rename_dl | Rename features in a data list |
| reorder_dl_uids | Reorder the uids in a data list |
| resample | Helper resampling function found in ?sample |
| run_snf | Run SNF |
| save_heatmap | Save a heatmap object to a file |
| scale_diagonals | Adjust the diagonals of a matrix |
| settings_df | Build a settings data frame |
| shiny_annotator | Launch a shiny app to identify meta cluster boundaries |
| similarity_matrix_heatmap | Plot heatmap of similarity matrix |
| similarity_matrix_path | Generate a complete path and filename to store an similarity... |
| sim_mats_list | Create or extract a 'sim_mats_list' class object |
| siw_euclidean_distance | Squared (including weights) Euclidean distance |
| snf_config | Define configuration for generating a set of SNF-based... |
| snf_scheme | SNF schemes |
| snf_step | Helper function for using the correct SNF scheme |
| sol_df_col_order | Helper function for organizing solutions df-like column order |
| solutions_df | Constructor for 'solutions_df' class object |
| split_parser | Helper function to determine which row and columns to split... |
| str.ari_matrix | Structure of a 'ari_matrix' object |
| str.clust_fns_list | Structure of a 'clust_fns_list' object |
| str.data_list | Structure of a 'data_list' object |
| str.dist_fns_list | Structure of a 'dist_fns_list' object |
| str.ext_solutions_df | Structure of a 'ext_solutions_df' object |
| str.settings_df | Structure of a 'settings_df' object |
| str.sim_mats_list | Structure of a 'sim_mats_list' object |
| str.snf_config | Structure of a 'snf_config' object |
| str.solutions_df | Structure of a 'solutions_df' object |
| str.t_ext_solutions_df | Structure of a 't_ext_solutions_df' object |
| str.t_solutions_df | Structure of a 't_solutions_df' object |
| str.weights_matrix | Structure of a 'weights_matrix' object |
| subc_v | Mock ABCD subcortical volumes data |
| subsample_dl | Create subsamples of a data list |
| subsample_pairwise_aris | Calculate pairwise adjusted Rand indices across subsamples of... |
| summarize_clust_fns_list | Summarize a clust_fns_list object |
| summarize_dfl | Summarize a distance functions list |
| summarize_dl | Summarize a data list |
| summarize_pvals | Summarize p-value columns of an extended solutions data frame |
| summary.ari_matrix | Summary method for class 'ari_matrix' |
| summary.clust_fns_list | Summary method for class 'clust_fns_list' |
| summary.data_list | Summary method for class 'data_list' |
| summary.dist_fns_list | Summary method for class 'dist_fns_list' |
| summary.ext_solutions_df | Summary method for class 'ext_solutions_df' |
| summary_features | Pull features used to calculate summary p-values from an... |
| summary.settings_df | Summary method for class 'settings_df' |
| summary.sim_mats_list | Summary method for class 'sim_mats_list' |
| summary.snf_config | Summary method for class 'snf_config' |
| summary.solutions_df | Summary method for class 'solutions_df' |
| summary.t_ext_solutions_df | Summary method for class 't_ext_solutions_df' |
| summary.t_solutions_df | Summary method for class 't_solutions_df' |
| summary.weights_matrix | Summary method for class 'weights_matrix' |
| train_test_assign | Training and testing split |
| uids | Pull UIDs from an object |
| validate_ari_matrix | Validator for 'ari_matrix' class object |
| validate_clust_fns_list | Validator for 'clust_fns_list' class object |
| validate_data_list | Validator for data_list class object |
| validate_dist_fns_list | Validator for dist_fns_list class object |
| validate_ext_solutions_df | Validator for 'ext_solutions_df' class object |
| validate_settings_df | Validator for 'settings_df' class object |
| validate_sim_mats_list | Validator for 'similarity_matrix_list' class object |
| validate_snf_config | Validator for snf_config class object |
| validate_solutions_df | Validator for 'solutions_df' class object |
| validate_weights_matrix | Validator for 'weights_matrix' class object |
| var_manhattan_plot | Manhattan plot of feature-feature association p-values |
| weights_matrix | Generate a matrix to store feature weights |
