[.ConsensusPartitionList
                        Subset a ConsensusPartitionList object
[.HierarchicalPartition
                        Subset the HierarchicalPartition object
[[.ConsensusPartitionList
                        Subset a ConsensusPartitionList object
[[.HierarchicalPartition
                        Subset the HierarchicalPartition object
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             Method dispatch page for cola_report
cola_report,ConsensusPartition-method
                        Make HTML report from the ConsensusPartition
                        object
cola_report,ConsensusPartitionList-method
                        Make HTML report from the
                        ConsensusPartitionList object
cola_report,HierarchicalPartition-method
                        Make HTML report from the HierarchicalPartition
                        object
cola_rl                 Example ConsensusPartitionList object
collect_classes         Method dispatch page for collect_classes
collect_classes,ConsensusPartition-method
                        Collect subgroups from ConsensusPartition
                        object
collect_classes,ConsensusPartitionList-method
                        Collect classes from ConsensusPartitionList
                        object
collect_classes,HierarchicalPartition-method
                        Collect classes from HierarchicalPartition
                        object
collect_plots           Method dispatch page for collect_plots
collect_plots,ConsensusPartition-method
                        Collect plots from ConsensusPartition object
collect_plots,ConsensusPartitionList-method
                        Collect plots from ConsensusPartitionList
                        object
collect_stats           Method dispatch page for collect_stats
collect_stats,ConsensusPartition-method
                        Draw and compare statistics for a single method
collect_stats,ConsensusPartitionList-method
                        Draw and compare statistics for multiple
                        methods
colnames                Method dispatch page for colnames
colnames,ConsensusPartition-method
                        Column names of the matrix
colnames,ConsensusPartitionList-method
                        Column names of the matrix
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      Method dispatch page for compare_signatures
compare_signatures,ConsensusPartition-method
                        Compare Signatures from Different k
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
dim.HierarchicalPartition
                        Dimension of the matrix
dimension_reduction     Method dispatch page for dimension_reduction
dimension_reduction,ConsensusPartition-method
                        Visualize column after 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
DownSamplingConsensusPartition-class
                        The DownSamplingConsensusPartition class
FCC                     Flatness of the CDF curve
find_best_km            Find a best k for the k-means clustering
functional_enrichment   Method dispatch page for functional_enrichment
functional_enrichment,ANY-method
                        Perform functional enrichment on signature
                        genes
functional_enrichment,ConsensusPartition-method
                        Perform functional enrichment on signature
                        genes
functional_enrichment,ConsensusPartitionList-method
                        Perform functional enrichment on signature
                        genes
functional_enrichment,HierarchicalPartition-method
                        Perform functional enrichment on signature
                        genes
get_anno                Method dispatch page for get_anno
get_anno_col            Method dispatch page for get_anno_col
get_anno_col,ConsensusPartition-method
                        Get annotation colors
get_anno_col,ConsensusPartitionList-method
                        Get annotation colors
get_anno_col,HierarchicalPartition-method
                        Get annotation colors
get_anno,ConsensusPartition-method
                        Get annotations
get_anno,ConsensusPartitionList-method
                        Get annotations
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             Method dispatch page for get_classes
get_classes,ConsensusPartition-method
                        Get subgroup labels
get_classes,ConsensusPartitionList-method
                        Get subgroup labels
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              Method dispatch page for get_matrix
get_matrix,ConsensusPartition-method
                        Get the original matrix
get_matrix,ConsensusPartitionList-method
                        Get the original matrix
get_matrix,DownSamplingConsensusPartition-method
                        Get the original matrix
get_matrix,HierarchicalPartition-method
                        Get the original matrix
get_membership          Method dispatch page for get_membership
get_membership,ConsensusPartition-method
                        Get membership matrix
get_membership,ConsensusPartitionList-method
                        Get membership matrix
get_param,ConsensusPartition-method
                        Get parameters
get_signatures          Method dispatch page for get_signatures
get_signatures,ConsensusPartition-method
                        Get signature rows
get_signatures,DownSamplingConsensusPartition-method
                        Get signature rows
get_signatures,HierarchicalPartition-method
                        Get signatures rows
get_stats               Method dispatch page for get_stats
get_stats,ConsensusPartition-method
                        Get statistics
get_stats,ConsensusPartitionList-method
                        Get statistics
golub_cola              Example ConsensusPartitionList object from
                        Golub dataset
golub_cola_ds           Example DownSamplingConsensusPartition object
                        from Golub dataset
golub_cola_rh           Example HierarchicalPartition object from Golub
                        dataset
hierarchical_partition
                        Hierarchical partition
HierarchicalPartition-class
                        The HierarchicalPartition class
is_best_k               Method dispatch page for is_best_k
is_best_k,ConsensusPartition-method
                        Test whether the current k is the best/optional
                        k
is_best_k,ConsensusPartitionList-method
                        Test whether the current k is the best/optional
                        k
is_leaf_node,HierarchicalPartition-method
                        Test whether a node is a leaf node
is_stable_k             Method dispatch page for is_stable_k
is_stable_k,ConsensusPartition-method
                        Test whether the current k corresponds to a
                        stable partition
is_stable_k,ConsensusPartitionList-method
                        Test whether the current k corresponds to a
                        stable partition
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_param        Parameters to merge branches in subgroup
                        dendrogram.
merge_node,HierarchicalPartition-method
                        Merge node
ncol                    Method dispatch page for ncol
ncol,ConsensusPartition-method
                        Number of columns in the matrix
ncol,ConsensusPartitionList-method
                        Number of columns in the matrix
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                    Method dispatch page for nrow
nrow,ConsensusPartition-method
                        Number of rows in the matrix
nrow,ConsensusPartitionList-method
                        Number of rows in the matrix
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 the consensus matrix
predict_classes         Method dispatch page for predict_classes
predict_classes,ConsensusPartition-method
                        Predict classes for new samples based on cola
                        classification
predict_classes,matrix-method
                        Predict classes for new samples based on
                        signature centroid matrix
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                Method dispatch page for rownames
rownames,ConsensusPartition-method
                        Row names of the matrix
rownames,ConsensusPartitionList-method
                        Row names of the matrix
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 subgroups
show                    Method dispatch page for show
show,ConsensusPartition-method
                        Print the ConsensusPartition object
show,ConsensusPartitionList-method
                        Print the ConsensusPartitionList object
show,DownSamplingConsensusPartition-method
                        Print the DownSamplingConsensusPartition object
show,HierarchicalPartition-method
                        Print the HierarchicalPartition object
split_node,HierarchicalPartition-method
                        Split node
suggest_best_k          Method dispatch page for suggest_best_k
suggest_best_k,ConsensusPartition-method
                        Suggest the best number of subgroups
suggest_best_k,ConsensusPartitionList-method
                        Suggest the best number of subgroups
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   Method dispatch page for test_to_known_factors
test_to_known_factors,ConsensusPartition-method
                        Test correspondance between predicted subgroups
                        and known factors
test_to_known_factors,ConsensusPartitionList-method
                        Test correspondance between predicted classes
                        and known factors
test_to_known_factors,DownSamplingConsensusPartition-method
                        Test correspondance between predicted subgroups
                        and known factors
test_to_known_factors,HierarchicalPartition-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,ConsensusPartition-method
                        Heatmap of top rows
top_rows_heatmap,ConsensusPartitionList-method
                        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
                        Heatmap of top rows from different top-value
                        methods
top_rows_overlap        Method dispatch page for top_rows_overlap
top_rows_overlap,ConsensusPartitionList-method
                        Overlap of top rows from different top-value
                        methods
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
