A Framework for Consensus and Hierarchical Partitioning


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Documentation for package ‘cola’ version 1.0.0

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A C D E G H K M P R S T V 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
ATC Ability to correlate other rows in the matrix (ATC score)

-- C --

cal_consensus Calculate consensus clustering related statistics
cola A bottle of cola
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_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
concordance Concordance of partitions 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 --

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

-- 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_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
guess_best_k Method dispatch page for guess_best_k
guess_best_k-method Guess the best number of partitions
guess_best_k-method Guess the best number of partitions
guess_best_k-method Guess the best number of partitions

-- 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 --

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

-- 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 --

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
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

-- 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

-- V --

venn_euler Make Venn Euler diagram from a list

-- misc --

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