# A Framework for Consensus Partitioning

## Documentation for package ‘cola’ version 2.0.0

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

## Help Pages

A C D E F G H I 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 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

## -- 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_rl | Example ConsensusPartitionList object
collect_classes | Method dispatch page for collect_classes
collect_classes-method | Collect subgroups 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
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
colnames-method | Column names of the matrix
compare_partitions | Compare two partitionings
compare_partitions-method | Compare two partitionings
compare_signatures | Method dispatch page for compare_signatures
compare_signatures-method | Compare Signatures from Different k
compare_signatures-method | Compare Signatures from Different Nodes
concordance | Concordance to the consensus partition
config_ATC | Adjust parameters for default ATC method
ConsensusPartition | The ConsensusPartition class
ConsensusPartition-class | The ConsensusPartition class
ConsensusPartitionList | The ConsensusPartitionList class
ConsensusPartitionList-class | The ConsensusPartitionList class
consensus_heatmap | Heatmap of the consensus matrix
consensus_heatmap-method | Heatmap of the consensus matrix
consensus_partition | Consensus partition
consensus_partition_by_down_sampling | Consensus partitioning only with a subset of columns
correspond_between_rankings | Correspond between a list of rankings
correspond_between_two_rankings | Correspond two rankings

## -- D --

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-method | Visualize column after 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
DownSamplingConsensusPartition | The DownSamplingConsensusPartition class
DownSamplingConsensusPartition-class | The DownSamplingConsensusPartition class

## -- 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
functional_enrichment | Method dispatch page for functional_enrichment
functional_enrichment-method | Perform functional enrichment on signature genes
functional_enrichment-method | Perform functional enrichment on signature genes
functional_enrichment-method | Perform functional enrichment on signature genes
functional_enrichment-method | Perform functional enrichment on signature genes

## -- 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-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_children_nodes | Test whether a node is a leaf node
get_children_nodes-method | Test whether a node is a leaf node
get_classes | Method dispatch page for get_classes
get_classes-method | Get subgroup labels
get_classes-method | Get subgroup labels
get_classes-method | Get subgroup labels
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 signature rows
get_signatures-method | Get signatures rows
get_stats | Method dispatch page for get_stats
get_stats-method | Get statistics
get_stats-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

## -- H --

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

## -- I --

is_best_k | Method dispatch page for is_best_k
is_best_k-method | Test whether the current k is the best/optional k
is_best_k-method | Test whether the current k is the best/optional k
is_leaf_node | Test whether a node is a leaf node
is_leaf_node-method | Test whether a node is a leaf node
is_stable_k | Method dispatch page for is_stable_k
is_stable_k-method | Test whether the current k corresponds to a stable partition
is_stable_k-method | Test whether the current k corresponds to a stable partition

## -- K --

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

## -- 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
merge_node | Merge node
merge_node-method | Merge node
merge_node_param | Parameters to merge branches in subgroup dendrogram.

## -- 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
ncol-method | Number of columns in the matrix
node_info | Information on the nodes
node_info-method | Information on the nodes
node_level | Information on the nodes
node_level-method | Information on the nodes
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 (eCDF) curve of the consensus matrix
plot_ecdf-method | Plot the empirical cumulative distribution (eCDF) curve of the consensus matrix
predict_classes | Method dispatch page for predict_classes
predict_classes-method | Predict classes for new samples based on cola classification
predict_classes-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

## -- R --

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-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 partitioning for all combinations of methods

## -- S --

select_partition_number | Several plots for determining the optimized number of subgroups
select_partition_number-method | Several plots for determining the optimized number of subgroups
show | Method dispatch page for show
show-method | Print the ConsensusPartition object
show-method | Print the ConsensusPartitionList object
show-method | Print the DownSamplingConsensusPartition object
show-method | Print the HierarchicalPartition object
split_node | Split node
split_node-method | Split node
suggest_best_k | Method dispatch page for suggest_best_k
suggest_best_k-method | Suggest the best number of subgroups
suggest_best_k-method | Suggest the best number of subgroups
suggest_best_k-method | Guess 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 subgroups 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 subgroups 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
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_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 on different nodes
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