All functions

ATC()

Ability to correlate to other rows

ATC_approx()

Ability to correlate to other rows - an approximated method

ConsensusPartition ConsensusPartition-class

The ConsensusPartition class

ConsensusPartitionList ConsensusPartitionList-class

The ConsensusPartitionList class

DownSamplingConsensusPartition DownSamplingConsensusPartition-class

The DownSamplingConsensusPartition class

`[`(<ConsensusPartitionList>)

Subset a ConsensusPartitionList object

`[`(<HierarchicalPartition>)

Subset the HierarchicalPartition object

`[[`(<ConsensusPartitionList>)

Subset a ConsensusPartitionList object

`[[`(<HierarchicalPartition>)

Subset the HierarchicalPartition object

FCC()

Flatness of the CDF curve

HierarchicalPartition HierarchicalPartition-class

The HierarchicalPartition class

PAC()

The proportion of ambiguous clustering (PAC score)

aPAC()

Adapted PAC scores

adjust_matrix()

Remove rows with low variance and impute missing values

adjust_outlier()

Adjust outliers

all_leaves(<HierarchicalPartition>)

All leaves in the hierarchy

all_nodes(<HierarchicalPartition>)

All nodes in the hierarchy

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(<ConsensusPartition>)

Make HTML report from the ConsensusPartition object

cola_report(<ConsensusPartitionList>)

Make HTML report from the ConsensusPartitionList object

cola_report(<HierarchicalPartition>)

Make HTML report from the HierarchicalPartition object

cola_report

Method dispatch page for cola_report

cola_rl

Example ConsensusPartitionList object

collect_classes(<ConsensusPartition>)

Collect subgroups from ConsensusPartition object

collect_classes(<ConsensusPartitionList>)

Collect classes from ConsensusPartitionList object

collect_classes(<HierarchicalPartition>)

Collect classes from HierarchicalPartition object

collect_classes

Method dispatch page for collect_classes

collect_plots(<ConsensusPartition>)

Collect plots from ConsensusPartition object

collect_plots(<ConsensusPartitionList>)

Collect plots from ConsensusPartitionList object

collect_plots

Method dispatch page for collect_plots

collect_stats(<ConsensusPartition>)

Draw and compare statistics for a single method

collect_stats(<ConsensusPartitionList>)

Draw and compare statistics for multiple methods

collect_stats

Method dispatch page for collect_stats

colnames(<ConsensusPartition>)

Column names of the matrix

colnames(<ConsensusPartitionList>)

Column names of the matrix

colnames(<DownSamplingConsensusPartition>)

Column names of the matrix

colnames(<HierarchicalPartition>)

Column names of the matrix

colnames

Method dispatch page for colnames

compare_partitions(<ConsensusPartition>)

Compare two partitionings

compare_signatures(<ConsensusPartition>)

Compare Signatures from Different k

compare_signatures(<HierarchicalPartition>)

Compare Signatures from Different Nodes

compare_signatures

Method dispatch page for compare_signatures

concordance()

Concordance to the consensus partition

config_ATC()

Adjust parameters for default ATC method

consensus_heatmap(<ConsensusPartition>)

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

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(<ConsensusPartition>)

Visualize column after dimension reduction

dimension_reduction(<DownSamplingConsensusPartition>)

Visualize column after dimension reduction

dimension_reduction(<HierarchicalPartition>)

Visualize columns after dimension reduction

dimension_reduction

Method dispatch page for dimension_reduction

dimension_reduction(<matrix>)

Visualize columns after dimension reduction

find_best_km()

Find a best k for the k-means clustering

functional_enrichment(<ANY>)

Perform functional enrichment on signature genes

functional_enrichment(<ConsensusPartition>)

Perform functional enrichment on signature genes

functional_enrichment(<ConsensusPartitionList>)

Perform functional enrichment on signature genes

functional_enrichment(<HierarchicalPartition>)

Perform functional enrichment on signature genes

functional_enrichment

Method dispatch page for functional_enrichment

get_anno(<ConsensusPartition>)

Get annotations

get_anno(<ConsensusPartitionList>)

Get annotations

get_anno(<DownSamplingConsensusPartition>)

Get annotations

get_anno(<HierarchicalPartition>)

Get annotations

get_anno

Method dispatch page for get_anno

get_anno_col(<ConsensusPartition>)

Get annotation colors

get_anno_col(<ConsensusPartitionList>)

Get annotation colors

get_anno_col(<HierarchicalPartition>)

Get annotation colors

get_anno_col

Method dispatch page for get_anno_col

get_children_nodes(<HierarchicalPartition>)

Test whether a node is a leaf node

get_classes(<ConsensusPartition>)

Get subgroup labels

get_classes(<ConsensusPartitionList>)

Get subgroup labels

get_classes(<DownSamplingConsensusPartition>)

Get subgroup labels

get_classes(<HierarchicalPartition>)

Get class IDs from the HierarchicalPartition object

get_classes

Method dispatch page for get_classes

get_consensus(<ConsensusPartition>)

Get consensus matrix

get_matrix(<ConsensusPartition>)

Get the original matrix

get_matrix(<ConsensusPartitionList>)

Get the original matrix

get_matrix(<DownSamplingConsensusPartition>)

Get the original matrix

get_matrix(<HierarchicalPartition>)

Get the original matrix

get_matrix

Method dispatch page for get_matrix

get_membership(<ConsensusPartition>)

Get membership matrix

get_membership(<ConsensusPartitionList>)

Get membership matrix

get_membership

Method dispatch page for get_membership

get_param(<ConsensusPartition>)

Get parameters

get_signatures(<ConsensusPartition>)

Get signature rows

get_signatures(<DownSamplingConsensusPartition>)

Get signature rows

get_signatures(<HierarchicalPartition>)

Get signatures rows

get_signatures

Method dispatch page for get_signatures

get_stats(<ConsensusPartition>)

Get statistics

get_stats(<ConsensusPartitionList>)

Get statistics

get_stats

Method dispatch page for get_stats

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

is_best_k(<ConsensusPartition>)

Test whether the current k is the best/optional k

is_best_k(<ConsensusPartitionList>)

Test whether the current k is the best/optional k

is_best_k

Method dispatch page for is_best_k

is_leaf_node(<HierarchicalPartition>)

Test whether a node is a leaf node

is_stable_k(<ConsensusPartition>)

Test whether the current k corresponds to a stable partition

is_stable_k(<ConsensusPartitionList>)

Test whether the current k corresponds to a stable partition

is_stable_k

Method dispatch page for is_stable_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

map_to_entrez_id()

Map to Entrez IDs

max_depth(<HierarchicalPartition>)

Max depth of the hierarchy

membership_heatmap(<ConsensusPartition>)

Heatmap of membership in each partition

merge_node(<HierarchicalPartition>)

Merge node

merge_node_param()

Parameters to merge branches in subgroup dendrogram.

ncol(<ConsensusPartition>)

Number of columns in the matrix

ncol(<ConsensusPartitionList>)

Number of columns in the matrix

ncol(<DownSamplingConsensusPartition>)

Number of columns in the matrix

ncol(<HierarchicalPartition>)

Number of columns in the matrix

ncol

Method dispatch page for ncol

node_info(<HierarchicalPartition>)

Information on the nodes

node_level(<HierarchicalPartition>)

Information on the nodes

nrow(<ConsensusPartition>)

Number of rows in the matrix

nrow(<ConsensusPartitionList>)

Number of rows in the matrix

nrow(<HierarchicalPartition>)

Number of rows in the matrix

nrow

Method dispatch page for nrow

plot_ecdf(<ConsensusPartition>)

Plot the empirical cumulative distribution (eCDF) curve of the consensus matrix

predict_classes(<ConsensusPartition>)

Predict classes for new samples based on cola classification

predict_classes

Method dispatch page for predict_classes

predict_classes(<matrix>)

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_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(<ConsensusPartition>)

Row names of the matrix

rownames(<ConsensusPartitionList>)

Row names of the matrix

rownames(<HierarchicalPartition>)

Row names of the matrix

rownames

Method dispatch page for rownames

run_all_consensus_partition_methods()

Consensus partitioning for all combinations of methods

select_partition_number(<ConsensusPartition>)

Several plots for determining the optimized number of subgroups

show(<ConsensusPartition>)

Print the ConsensusPartition object

show(<ConsensusPartitionList>)

Print the ConsensusPartitionList object

show(<DownSamplingConsensusPartition>)

Print the DownSamplingConsensusPartition object

show(<HierarchicalPartition>)

Print the HierarchicalPartition object

show

Method dispatch page for show

split_node(<HierarchicalPartition>)

Split node

suggest_best_k(<ConsensusPartition>)

Suggest the best number of subgroups

suggest_best_k(<ConsensusPartitionList>)

Suggest the best number of subgroups

suggest_best_k(<HierarchicalPartition>)

Guess the best number of partitions

suggest_best_k

Method dispatch page for suggest_best_k

test_between_factors()

Test whether a list of factors are correlated

test_to_known_factors(<ConsensusPartition>)

Test correspondance between predicted subgroups and known factors

test_to_known_factors(<ConsensusPartitionList>)

Test correspondance between predicted classes and known factors

test_to_known_factors(<DownSamplingConsensusPartition>)

Test correspondance between predicted subgroups and known factors

test_to_known_factors(<HierarchicalPartition>)

Test correspondance between predicted classes and known factors

test_to_known_factors

Method dispatch page for test_to_known_factors

top_elements_overlap()

Overlap of top elements from different metrics

top_rows_heatmap(<ConsensusPartition>)

Heatmap of top rows

top_rows_heatmap(<ConsensusPartitionList>)

Heatmap of top rows from different top-value methods

top_rows_heatmap(<HierarchicalPartition>)

Heatmap of top rows from different top-value methods

top_rows_heatmap

Method dispatch page for top_rows_heatmap

top_rows_heatmap(<matrix>)

Heatmap of top rows from different top-value methods

top_rows_overlap(<ConsensusPartitionList>)

Overlap of top rows from different top-value methods

top_rows_overlap(<HierarchicalPartition>)

Overlap of top rows on different nodes

top_rows_overlap

Method dispatch page for top_rows_overlap

top_rows_overlap(<matrix>)

Overlap of top rows from different top-value methods