A Framework for Consensus and Hierarchical Partitioning


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Documentation for package ‘cola’ version 1.0.1

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A C D E F G H 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 partition methods
all_top_value_methods All supported top-value methods
aPAC Adapted PAC scores
ATC Ability to correlate other rows in the matrix

-- 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_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_plots-method Collect plots from HierarchicalPartition 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
compare_signatures Compare Signatures from Different k
compare_signatures-method Compare Signatures from Different k
concordance Concordance 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 --

dim.ConsensusPartition Dimension of the matrix
dim.ConsensusPartitionList 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 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

-- F --

FCC Flatness of the CDF curve
find_best_km Find a best k for the k-means clustering

-- 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_hierarchy Get the partition hierarchy
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
GO_enrichment Method dispatch page for GO_enrichment
GO_enrichment-method Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method Perform Gene Ontology Enrichment on Signature Genes
GO_enrichment-method Perform Gene Ontology Enrichment on Signature Genes

-- 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 --

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

-- 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
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 curve (ECDF) of the consensus matrix
plot_ecdf-method Plot the empirical cumulative distribution curve (ECDF) of the consensus matrix

-- R --

recalc_stats Recalculate statistics in the ConsensusPartitionList object
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
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 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
suggest_best_k Method dispatch page for suggest_best_k
suggest_best_k-method Suggest the best number of partitions
suggest_best_k-method Suggest the best number of partitions
suggest_best_k-method Suggest 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 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

-- misc --

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