# A Framework for Consensus and Hierarchical Partitioning

## Documentation for package ‘cola’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H K M N P R S T misc

## -- A --

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
aPAC | Adapted PAC scores
ATC | Ability to correlate other rows in the matrix

## -- C --

cola | A bottle of cola
cola_opt | Global Parameters
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_plots-method | Collect plots from HierarchicalPartition 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
colnames | Method dispatch page for colnames
colnames-method | Column names of the matrix
colnames-method | Column names of the matrix
colnames-method | Column names of the matrix
compare_signatures | Compare Signatures from Different k
compare_signatures-method | Compare Signatures from Different k
concordance | Concordance 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

## -- D --

dim.ConsensusPartition | Dimension of the matrix
dim.ConsensusPartitionList | Dimension of the matrix
dim.HierarchicalPartition | Dimension of the matrix
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

## -- E --

Extract.ConsensusPartitionList | Subset a ConsensusPartitionList object
Extract.HierarchicalPartition | Subset the HierarchicalPartition object
ExtractExtract.ConsensusPartitionList | Subset a ConsensusPartitionList object
ExtractExtract.HierarchicalPartition | Subset the HierarchicalPartition object

## -- F --

FCC | Flatness of the CDF curve
find_best_km | Find a best k for the k-means clustering

## -- G --

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_hierarchy | Get the partition hierarchy
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
GO_enrichment | Method dispatch page for GO_enrichment
GO_enrichment-method | Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method | Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method | Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method | Perform Gene Ontology Enrichment on Signature Genes

## -- H --

HierarchicalPartition | The HierarchicalPartition class
HierarchicalPartition-class | The HierarchicalPartition class
hierarchical_partition | Hierarchical partition

## -- K --

knitr_add_tab_item | Add one JavaScript tab in the report
knitr_insert_tabs | Generate the HTML fragment for the JavaScript tabs.

## -- M --

map_to_entrez_id | Map to Entrez IDs
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

## -- N --

ncol | Method dispatch page for ncol
ncol-method | Number of columns in the matrix
ncol-method | Number of columns in the matrix
ncol-method | Number of columns in the matrix
nrow | Method dispatch page for nrow
nrow-method | Number of rows in the matrix
nrow-method | Number of rows in the matrix
nrow-method | Number of rows in the matrix

## -- P --

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

## -- R --

recalc_stats | Recalculate statistics in the ConsensusPartitionList object
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
rownames | Method dispatch page for rownames
rownames-method | Row names of the matrix
rownames-method | Row names of the matrix
rownames-method | Row names of the matrix
run_all_consensus_partition_methods | Consensus partition for all combinations of methods

## -- S --

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
suggest_best_k | Method dispatch page for suggest_best_k
suggest_best_k-method | Suggest the best number of partitions
suggest_best_k-method | Suggest the best number of partitions
suggest_best_k-method | Suggest the best number of partitions

## -- T --

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

## -- misc --

[.ConsensusPartitionList | Subset a ConsensusPartitionList object
[.HierarchicalPartition | Subset the HierarchicalPartition object
[[.ConsensusPartitionList | Subset a ConsensusPartitionList object
[[.HierarchicalPartition | Subset the HierarchicalPartition object