Man pages for jokergoo/cola
A Framework for Consensus Partitioning
| adjust_matrix | Remove rows with low variance and impute missing values |
| adjust_outlier | Adjust outliers |
| all_leaves-HierarchicalPartition-method | All leaves in the hierarchy |
| all_nodes-HierarchicalPartition-method | All nodes in the hierarchy |
| all_partition_methods | All supported partitioning methods |
| all_top_value_methods | All supported top-value methods |
| aPAC | Adapted PAC scores |
| ATC | Ability to correlate to other rows |
| ATC_approx | Ability to correlate to other rows - an approximated method |
| cola | A bottle of cola |
| cola_opt | Global parameters |
| cola_report-ConsensusPartitionList-method | Make HTML report from the ConsensusPartitionList object |
| cola_report-ConsensusPartition-method | Make HTML report from the ConsensusPartition object |
| cola_report-dispatch | Method dispatch page for cola_report |
| cola_report-HierarchicalPartition-method | Make HTML report from the HierarchicalPartition object |
| cola_rl | Example ConsensusPartitionList object |
| collect_classes-ConsensusPartitionList-method | Collect classes from ConsensusPartitionList object |
| collect_classes-ConsensusPartition-method | Collect subgroups from ConsensusPartition object |
| collect_classes-dispatch | Method dispatch page for collect_classes |
| collect_classes-HierarchicalPartition-method | Collect classes from HierarchicalPartition object |
| collect_plots-ConsensusPartitionList-method | Collect plots from ConsensusPartitionList object |
| collect_plots-ConsensusPartition-method | Collect plots from ConsensusPartition object |
| collect_plots-dispatch | Method dispatch page for collect_plots |
| collect_stats-ConsensusPartitionList-method | Draw and compare statistics for multiple methods |
| collect_stats-ConsensusPartition-method | Draw and compare statistics for a single method |
| collect_stats-dispatch | Method dispatch page for collect_stats |
| colnames-ConsensusPartitionList-method | Column names of the matrix |
| colnames-ConsensusPartition-method | Column names of the matrix |
| colnames-dispatch | Method dispatch page for colnames |
| colnames-DownSamplingConsensusPartition-method | Column names of the matrix |
| colnames-HierarchicalPartition-method | Column names of the matrix |
| compare_partitions-ConsensusPartition-method | Compare two partitionings |
| compare_signatures-ConsensusPartition-method | Compare Signatures from Different k |
| compare_signatures-dispatch | Method dispatch page for compare_signatures |
| compare_signatures-HierarchicalPartition-method | Compare Signatures from Different Nodes |
| concordance | Concordance to the consensus partition |
| config_ATC | Adjust parameters for default ATC method |
| consensus_heatmap-ConsensusPartition-method | Heatmap of the consensus matrix |
| consensus_partition | Consensus partition |
| consensus_partition_by_down_sampling | Consensus partitioning only with a subset of columns |
| ConsensusPartition-class | The ConsensusPartition class |
| ConsensusPartitionList-class | The ConsensusPartitionList class |
| correspond_between_rankings | Correspond between a list of rankings |
| correspond_between_two_rankings | Correspond two rankings |
| david_enrichment | Perform DAVID enrichment analysis |
| dim.ConsensusPartition | Dimension of the matrix |
| dim.ConsensusPartitionList | Dimension of the matrix |
| dim.DownSamplingConsensusPartition | Dimension of the matrix |
| dimension_reduction-ConsensusPartition-method | Visualize column after dimension reduction |
| dimension_reduction-dispatch | Method dispatch page for dimension_reduction |
| dimension_reduction-DownSamplingConsensusPartition-method | Visualize column after dimension reduction |
| dimension_reduction-HierarchicalPartition-method | Visualize columns after dimension reduction |
| dimension_reduction-matrix-method | Visualize columns after dimension reduction |
| dim.HierarchicalPartition | Dimension of the matrix |
| DownSamplingConsensusPartition-class | The DownSamplingConsensusPartition class |
| Extract.ConsensusPartitionList | Subset a ConsensusPartitionList object |
| ExtractExtract.ConsensusPartitionList | Subset a ConsensusPartitionList object |
| ExtractExtract.HierarchicalPartition | Subset the HierarchicalPartition object |
| Extract.HierarchicalPartition | Subset the HierarchicalPartition object |
| FCC | Flatness of the CDF curve |
| find_best_km | Find a best k for the k-means clustering |
| functional_enrichment-ANY-method | Perform functional enrichment on signature genes |
| functional_enrichment-ConsensusPartitionList-method | Perform functional enrichment on signature genes |
| functional_enrichment-ConsensusPartition-method | Perform functional enrichment on signature genes |
| functional_enrichment-dispatch | Method dispatch page for functional_enrichment |
| functional_enrichment-HierarchicalPartition-method | Perform functional enrichment on signature genes |
| get_anno_col-ConsensusPartitionList-method | Get annotation colors |
| get_anno_col-ConsensusPartition-method | Get annotation colors |
| get_anno_col-dispatch | Method dispatch page for get_anno_col |
| get_anno_col-HierarchicalPartition-method | Get annotation colors |
| get_anno-ConsensusPartitionList-method | Get annotations |
| get_anno-ConsensusPartition-method | Get annotations |
| get_anno-dispatch | Method dispatch page for get_anno |
| get_anno-DownSamplingConsensusPartition-method | Get annotations |
| get_anno-HierarchicalPartition-method | Get annotations |
| get_children_nodes-HierarchicalPartition-method | Test whether a node is a leaf node |
| get_classes-ConsensusPartitionList-method | Get subgroup labels |
| get_classes-ConsensusPartition-method | Get subgroup labels |
| get_classes-dispatch | Method dispatch page for get_classes |
| get_classes-DownSamplingConsensusPartition-method | Get subgroup labels |
| get_classes-HierarchicalPartition-method | Get class IDs from the HierarchicalPartition object |
| get_consensus-ConsensusPartition-method | Get consensus matrix |
| get_matrix-ConsensusPartitionList-method | Get the original matrix |
| get_matrix-ConsensusPartition-method | Get the original matrix |
| get_matrix-dispatch | Method dispatch page for get_matrix |
| get_matrix-DownSamplingConsensusPartition-method | Get the original matrix |
| get_matrix-HierarchicalPartition-method | Get the original matrix |
| get_membership-ConsensusPartitionList-method | Get membership matrix |
| get_membership-ConsensusPartition-method | Get membership matrix |
| get_membership-dispatch | Method dispatch page for get_membership |
| get_param-ConsensusPartition-method | Get parameters |
| get_signatures-ConsensusPartition-method | Get signature rows |
| get_signatures-dispatch | Method dispatch page for get_signatures |
| get_signatures-DownSamplingConsensusPartition-method | Get signature rows |
| get_signatures-HierarchicalPartition-method | Get signatures rows |
| get_stats-ConsensusPartitionList-method | Get statistics |
| get_stats-ConsensusPartition-method | Get statistics |
| get_stats-dispatch | Method dispatch page for get_stats |
| golub_cola | Example ConsensusPartitionList object from Golub dataset |
| golub_cola_ds | Example DownSamplingConsensusPartition object from Golub... |
| golub_cola_rh | Example HierarchicalPartition object from Golub dataset |
| hierarchical_partition | Hierarchical partition |
| HierarchicalPartition-class | The HierarchicalPartition class |
| is_best_k-ConsensusPartitionList-method | Test whether the current k is the best/optional k |
| is_best_k-ConsensusPartition-method | Test whether the current k is the best/optional k |
| is_best_k-dispatch | Method dispatch page for is_best_k |
| is_leaf_node-HierarchicalPartition-method | Test whether a node is a leaf node |
| is_stable_k-ConsensusPartitionList-method | Test whether the current k corresponds to a stable partition |
| is_stable_k-ConsensusPartition-method | Test whether the current k corresponds to a stable partition |
| is_stable_k-dispatch | Method dispatch page for is_stable_k |
| knee_finder2 | Find the knee/elbow of a list of sorted points |
| knitr_add_tab_item | Add JavaScript tab in the report |
| knitr_insert_tabs | Generate the HTML fragment for the JavaScript tabs |
| map_to_entrez_id | Map to Entrez IDs |
| max_depth-HierarchicalPartition-method | Max depth of the hierarchy |
| membership_heatmap-ConsensusPartition-method | Heatmap of membership in each partition |
| merge_node-HierarchicalPartition-method | Merge node |
| merge_node_param | Parameters to merge branches in subgroup dendrogram. |
| ncol-ConsensusPartitionList-method | Number of columns in the matrix |
| ncol-ConsensusPartition-method | Number of columns in the matrix |
| ncol-dispatch | Method dispatch page for ncol |
| ncol-DownSamplingConsensusPartition-method | Number of columns in the matrix |
| ncol-HierarchicalPartition-method | Number of columns in the matrix |
| node_info-HierarchicalPartition-method | Information on the nodes |
| node_level-HierarchicalPartition-method | Information on the nodes |
| nrow-ConsensusPartitionList-method | Number of rows in the matrix |
| nrow-ConsensusPartition-method | Number of rows in the matrix |
| nrow-dispatch | Method dispatch page for nrow |
| nrow-HierarchicalPartition-method | Number of rows in the matrix |
| PAC | The proportion of ambiguous clustering (PAC score) |
| plot_ecdf-ConsensusPartition-method | Plot the empirical cumulative distribution (eCDF) curve of... |
| predict_classes-ConsensusPartition-method | Predict classes for new samples based on cola classification |
| predict_classes-dispatch | Method dispatch page for predict_classes |
| predict_classes-matrix-method | Predict classes for new samples based on signature centroid... |
| print.hc_table_suggest_best_k | Print the hc_table_suggest_best_k object |
| recalc_stats | Recalculate statistics in the ConsensusPartitionList object |
| register_NMF | Register NMF partitioning method |
| register_partition_methods | Register user-defined partitioning methods |
| register_SOM | Register SOM partitioning method |
| register_top_value_methods | Register user-defined top-value methods |
| relabel_class | Relabel class labels according to the reference labels |
| remove_partition_methods | Remove partitioning methods |
| remove_top_value_methods | Remove top-value methods |
| rownames-ConsensusPartitionList-method | Row names of the matrix |
| rownames-ConsensusPartition-method | Row names of the matrix |
| rownames-dispatch | Method dispatch page for rownames |
| rownames-HierarchicalPartition-method | Row names of the matrix |
| run_all_consensus_partition_methods | Consensus partitioning for all combinations of methods |
| select_partition_number-ConsensusPartition-method | Several plots for determining the optimized number of... |
| show-ConsensusPartitionList-method | Print the ConsensusPartitionList object |
| show-ConsensusPartition-method | Print the ConsensusPartition object |
| show-dispatch | Method dispatch page for show |
| show-DownSamplingConsensusPartition-method | Print the DownSamplingConsensusPartition object |
| show-HierarchicalPartition-method | Print the HierarchicalPartition object |
| split_node-HierarchicalPartition-method | Split node |
| suggest_best_k-ConsensusPartitionList-method | Suggest the best number of subgroups |
| suggest_best_k-ConsensusPartition-method | Suggest the best number of subgroups |
| suggest_best_k-dispatch | Method dispatch page for suggest_best_k |
| suggest_best_k-HierarchicalPartition-method | Guess the best number of partitions |
| test_between_factors | Test whether a list of factors are correlated |
| test_to_known_factors-ConsensusPartitionList-method | Test correspondance between predicted classes and known... |
| test_to_known_factors-ConsensusPartition-method | Test correspondance between predicted subgroups and known... |
| test_to_known_factors-dispatch | Method dispatch page for test_to_known_factors |
| test_to_known_factors-DownSamplingConsensusPartition-method | Test correspondance between predicted subgroups and known... |
| test_to_known_factors-HierarchicalPartition-method | Test correspondance between predicted classes and known... |
| top_elements_overlap | Overlap of top elements from different metrics |
| top_rows_heatmap-ConsensusPartitionList-method | Heatmap of top rows from different top-value methods |
| top_rows_heatmap-ConsensusPartition-method | Heatmap of top rows |
| top_rows_heatmap-dispatch | Method dispatch page for top_rows_heatmap |
| top_rows_heatmap-HierarchicalPartition-method | Heatmap of top rows from different top-value methods |
| top_rows_heatmap-matrix-method | Heatmap of top rows from different top-value methods |
| top_rows_overlap-ConsensusPartitionList-method | Overlap of top rows from different top-value methods |
| top_rows_overlap-dispatch | Method dispatch page for top_rows_overlap |
| top_rows_overlap-HierarchicalPartition-method | Overlap of top rows on different nodes |
| top_rows_overlap-matrix-method | Overlap of top rows from different top-value methods |
