ATC                     Ability to correlate to other rows
ConsensusPartition-class
                        The ConsensusPartition class
ConsensusPartitionList-class
                        The ConsensusPartitionList class
FCC                     Flatness of the CDF curve
PAC                     The proportion of ambiguous clustering (PAC
                        score)
[.ConsensusPartitionList
                        Subset a ConsensusPartitionList object
[[.ConsensusPartitionList
                        Subset a ConsensusPartitionList object
aPAC                    Adapted PAC scores
adjust_matrix           Remove rows with low variance and impute
                        missing values
adjust_outlier          Adjust outliers
all_partition_methods   All supported partitioning methods
all_top_value_methods   All supported top-value methods
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_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_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
compare_signatures,ConsensusPartition-method
                        Compare Signatures from Different k
concordance             Concordance to the consensus partition
consensus_heatmap,ConsensusPartition-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
dim.ConsensusPartition
                        Dimension of the matrix
dim.ConsensusPartitionList
                        Dimension of the matrix
dimension_reduction     Method dispatch page for dimension_reduction
dimension_reduction,ConsensusPartition-method
                        Visualize column after dimension reduction
dimension_reduction,matrix-method
                        Visualize columns after dimension reduction
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
get_anno                Method dispatch page for get_anno
get_anno,ConsensusPartition-method
                        Get annotations
get_anno,ConsensusPartitionList-method
                        Get annotations
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_classes             Method dispatch page for get_classes
get_classes,ConsensusPartition-method
                        Get subgroup labels
get_classes,ConsensusPartitionList-method
                        Get subgroup labels
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_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,ConsensusPartition-method
                        Get signature rows
get_stats               Method dispatch page for get_stats
get_stats,ConsensusPartition-method
                        Get statistics
get_stats,ConsensusPartitionList-method
                        Get statistics
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_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
knitr_add_tab_item      Add one JavaScript tab in the report
knitr_insert_tabs       Generate the HTML fragment for the JavaScript
                        tabs
map_to_entrez_id        Map to Entrez IDs
membership_heatmap,ConsensusPartition-method
                        Heatmap of membership in each partition
ncol                    Method dispatch page for ncol
ncol,ConsensusPartition-method
                        Number of columns in the matrix
ncol,ConsensusPartitionList-method
                        Number of columns in the matrix
nrow                    Method dispatch page for nrow
nrow,ConsensusPartition-method
                        Number of rows in the matrix
nrow,ConsensusPartitionList-method
                        Number of rows in the matrix
plot_ecdf,ConsensusPartition-method
                        Plot the empirical cumulative distribution
                        curve (eCDF) of the consensus matrix
recalc_stats            Recalculate statistics in the
                        ConsensusPartitionList object
register_NMF            Register NMF partitioning method
register_SOM            Register SOM partitioning method
register_partition_methods
                        Register user-defined partitioning methods
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
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
submit_to_david         Perform DAVID analysis
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
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
top_elements_overlap    Overlap of top elements from different metrics
top_rows_heatmap        Method dispatch page for top_rows_heatmap
top_rows_heatmap,ConsensusPartitionList-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,matrix-method
                        Overlap of top rows from different top-value
                        methods
