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