A Framework for Consensus Partitioning


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Documentation for package ‘cola’ version 2.2.0

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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