A Framework for Consensus Partitioning

Documentation for package ‘cola’ version 2.4.0

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-- 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