A C D E G H K M P R S T V misc
adjust_matrix | Remove rows with low variance and impute missing values |
adjust_outlier | Adjust outliers |
all_leaves | All leaves in the hierarchy |
all_leaves-method | All leaves in the hierarchy |
all_nodes | All nodes in the hierarchy |
all_nodes-method | All nodes in the hierarchy |
all_partition_methods | All supported partition methods |
all_top_value_methods | All supported top-value methods |
ATC | Ability to correlate other rows in the matrix (ATC score) |
cal_consensus | Calculate consensus clustering related statistics |
cola | A bottle of cola |
cola_report | Method dispatch page for cola_report |
cola_report-method | Make HTML report from the ConsensusPartition object |
cola_report-method | Make HTML report from the ConsensusPartitionList object |
cola_report-method | Make HTML report from the HierarchicalPartition object |
cola_rh | Example HierarchicalPartition object |
cola_rl | Example ConsensusPartitionList object |
collect_classes | Method dispatch page for collect_classes |
collect_classes-method | Collect classes from ConsensusPartition object |
collect_classes-method | Collect classes from ConsensusPartitionList object |
collect_classes-method | Collect classes from HierarchicalPartition object |
collect_plots | Method dispatch page for collect_plots |
collect_plots-method | Collect plots from ConsensusPartition object |
collect_plots-method | Collect plots from ConsensusPartitionList object |
collect_stats | Method dispatch page for collect_stats |
collect_stats-method | Draw and compare statistics for a single method |
collect_stats-method | Draw and compare statistics for multiple methods |
concordance | Concordance of partitions to the consensus partition |
ConsensusPartition | The ConsensusPartition class |
ConsensusPartition-class | The ConsensusPartition class |
ConsensusPartitionList | The ConsensusPartitionList class |
ConsensusPartitionList-class | The ConsensusPartitionList class |
consensus_heatmap | Heatmap for the consensus matrix |
consensus_heatmap-method | Heatmap for the consensus matrix |
consensus_partition | Consensus partition |
correspond_between_rankings | Correspond between a list of rankings |
correspond_between_two_rankings | Correspond two rankings |
dimension_reduction | Method dispatch page for dimension_reduction |
dimension_reduction-method | Visualize column after dimension reduction |
dimension_reduction-method | Visualize columns after dimension reduction |
dimension_reduction-method | Visualize columns after dimension reduction |
Extract.ConsensusPartitionList | Subset a ConsensusPartitionList object |
Extract.HierarchicalPartition | Subset the HierarchicalPartition object |
ExtractExtract.ConsensusPartitionList | Subset a ConsensusPartitionList object |
ExtractExtract.HierarchicalPartition | Subset the HierarchicalPartition object |
get_anno | Method dispatch page for get_anno |
get_anno-method | Get annotations |
get_anno-method | Get annotations |
get_anno-method | Get annotations |
get_anno_col | Method dispatch page for get_anno_col |
get_anno_col-method | Get annotation colors |
get_anno_col-method | Get annotation colors |
get_anno_col-method | Get annotation colors |
get_classes | Method dispatch page for get_classes |
get_classes-method | Get class IDs from the ConsensusPartition object |
get_classes-method | Get class IDs from the ConsensusPartitionList object |
get_classes-method | Get class IDs from the HierarchicalPartition object |
get_consensus | Get consensus matrix |
get_consensus-method | Get consensus matrix |
get_matrix | Method dispatch page for get_matrix |
get_matrix-method | Get the original matrix |
get_matrix-method | Get the original matrix |
get_matrix-method | Get the original matrix |
get_membership | Method dispatch page for get_membership |
get_membership-method | Get membership matrix |
get_membership-method | Get membership matrix |
get_param | Get parameters |
get_param-method | Get parameters |
get_signatures | Method dispatch page for get_signatures |
get_signatures-method | Get signature rows |
get_signatures-method | Get signatures rows |
get_stats | Method dispatch page for get_stats |
get_stats-method | Get statistics for the consensus partition |
get_stats-method | Get statistics for consensus partitions from all methods |
guess_best_k | Method dispatch page for guess_best_k |
guess_best_k-method | Guess the best number of partitions |
guess_best_k-method | Guess the best number of partitions |
guess_best_k-method | Guess the best number of partitions |
HierarchicalPartition | The HierarchicalPartition class |
HierarchicalPartition-class | The HierarchicalPartition class |
hierarchical_partition | Hierarchical partition |
knitr_add_tab_item | Add one JavaScript tab in the report |
knitr_insert_tabs | Generate the HTML fragment for the JavaScript tabs. |
max_depth | Max depth of the hierarchy |
max_depth-method | Max depth of the hierarchy |
membership_heatmap | Heatmap of membership in each partition |
membership_heatmap-method | Heatmap of membership in each partition |
PAC | The proportion of ambiguous clustering (PAC score) |
plot_ecdf | Plot the empirical cumulative distribution curve (ECDF) of the consensus matrix |
plot_ecdf-method | Plot the empirical cumulative distribution curve (ECDF) of the consensus matrix |
register_NMF | Register NMF partition method |
register_partition_methods | Register user-defined partition functions |
register_SOM | Register SOM partition method |
register_top_value_methods | Register user-defined top-value methods |
relabel_class | Relabel class IDs according to the reference ID |
remove_partition_methods | Remove partition methods |
remove_top_value_methods | Remove top-value methods |
run_all_consensus_partition_methods | Consensus partition for all combinations of methods |
select_partition_number | Several plots for determining the optimized number of partitions |
select_partition_number-method | Several plots for determining the optimized number of partitions |
show | Method dispatch page for show |
show-method | Print the ConsensusPartition object |
show-method | Print the ConsensusPartitionList object |
show-method | Print the HierarchicalPartition object |
submit_to_david | Perform DAVID analysis |
test_between_factors | Test whether a list of factors are correlated |
test_to_known_factors | Method dispatch page for test_to_known_factors |
test_to_known_factors-method | Test correspondance between predicted classes and known factors |
test_to_known_factors-method | Test correspondance between predicted classes and known factors |
test_to_known_factors-method | Test correspondance between predicted classes and known factors |
top_elements_overlap | Overlap of top elements from different metrics |
top_rows_heatmap | Method dispatch page for top_rows_heatmap |
top_rows_heatmap-method | Heatmap of top rows from different top-value methods |
top_rows_heatmap-method | Heatmap of top rows from different top-value methods |
top_rows_overlap | Method dispatch page for top_rows_overlap |
top_rows_overlap-method | Overlap of top rows from different top-value methods |
top_rows_overlap-method | Overlap of top rows from different top-value methods |
venn_euler | Make Venn Euler diagram from a list |
[.ConsensusPartitionList | Subset a ConsensusPartitionList object |
[.HierarchicalPartition | Subset the HierarchicalPartition object |
[[.ConsensusPartitionList | Subset a ConsensusPartitionList object |
[[.HierarchicalPartition | Subset the HierarchicalPartition object |