Man pages for jokergoo/cola
A Framework for Consensus and Hierarchical Partition

AACAAC score
adjust_matrixRemove rows with low variance and impute missing data
adjust_outlierAdjust outliers
all_leaves-HierarchicalPartition-methodAll leaves in the hierarchy
all_nodes-HierarchicalPartition-methodAll nodes in the hierarchy
all_partition_methodsAll supported partition methods
all_top_value_methodsAll supported top value methods
colaA bottle of cola
cola_report-ConsensusPartitionList-methodMake report for the ConsensusPartitionList object
cola_report-ConsensusPartition-methodMake report for the ConsensusPartition object
cola_report-dispatchMethod dispatch page for cola_report
cola_report-HierarchicalPartition-methodMake report for the HierarchicalPartition object
cola_rhExample for HierarchicalPartition object
cola_rlExample for ConsensusPartitionList object
collect_classes-ConsensusPartitionList-methodCollect classes from ConsensusPartitionList object
collect_classes-ConsensusPartition-methodCollect classes from ConsensusPartition object
collect_classes-dispatchMethod dispatch page for collect_classes
collect_classes-HierarchicalPartition-methodCollect classes from hierarchical_partition object
collect_plots-ConsensusPartitionList-methodCollect plots from ConsensusPartitionList object
collect_plots-ConsensusPartition-methodCollect plots from ConsensusPartition object
collect_plots-dispatchMethod dispatch page for collect_plots
concordanceConcordance of partitions to the consensus partition
consensus_heatmap-ConsensusPartition-methodHeatmap for the consensus matrix
consensus_partitionConsensus partition
ConsensusPartition-classThe ConsensusPartition class
ConsensusPartitionList-classThe ConsensusPartitionList class
correspond_between_rankingsCorrespond between a list of rankings
correspond_between_two_rankingsCorrespond two rankings
dimension_reduction-ConsensusPartition-methodVisualize samples after dimension reduction
dimension_reduction-dispatchMethod dispatch page for dimension_reduction
dimension_reduction-HierarchicalPartition-methodVisualize columns after dimension reduction
dimension_reduction-matrix-methodVisualize columns after dimension reduction
Extract.ConsensusPartitionListSubset a ConsensusPartitionList object
ExtractExtract.HierarchicalPartitionSubset the HierarchicalPartition object
Extract.HierarchicalPartitionSubset the HierarchicalPartition object
get_anno_col-ConsensusPartitionList-methodGet annotation colors
get_anno_col-ConsensusPartition-methodGet annotation colors
get_anno_col-dispatchMethod dispatch page for get_anno_col
get_anno_col-HierarchicalPartition-methodGet annotation colors
get_anno-ConsensusPartitionList-methodGet annotations
get_anno-ConsensusPartition-methodGet annotations
get_anno-dispatchMethod dispatch page for get_anno
get_anno-HierarchicalPartition-methodGet annotations
get_classes-ConsensusPartitionList-methodGet class from the ConsensusPartitionList object
get_classes-ConsensusPartition-methodGet class from the ConsensusPartition object
get_classes-dispatchMethod dispatch page for get_classes
get_classes-HierarchicalPartition-methodGet class from the HierarchicalPartition object
get_consensus-ConsensusPartition-methodGet consensus matrix
get_matrix-ConsensusPartitionList-methodGet original matrix
get_matrix-ConsensusPartition-methodGet original matrix
get_matrix-dispatchMethod dispatch page for get_matrix
get_matrix-HierarchicalPartition-methodGet the original matrix
get_membership-ConsensusPartitionList-methodGet membership matrix
get_membership-ConsensusPartition-methodGet membership matrix
get_membership-dispatchMethod dispatch page for get_membership
get_param-ConsensusPartition-methodGet parameters
get_signatures-ConsensusPartition-methodGet signature rows
get_signatures-dispatchMethod dispatch page for get_signatures
get_signatures-HierarchicalPartition-methodGet signatures rows
get_stat-ConsensusPartitionList-methodGet statistics
get_stat-ConsensusPartition-methodGet statistics
get_stat-dispatchMethod dispatch page for get_stat
guess_best_k-ConsensusPartitionList-methodGet the best number of partitions
guess_best_k-ConsensusPartition-methodGuess the best number of partitions
guess_best_k-dispatchMethod dispatch page for guess_best_k
hierarchical_partitionHierarchical detection of subgroups
HierarchicalPartition-classThe HierarchicalPartition class
knitr_add_tab_itemAdd one JavaScript tab in the report
knitr_insert_tabsGenerate the HTML code for the JavaScript tabs.
max_depth-HierarchicalPartition-methodMax depth of the hierarchy
membership_heatmap-ConsensusPartition-methodHeatmap of membership of samples in each partition
PACPAC score
plot_ecdf-ConsensusPartition-methodPlot the empirical cumulative distribution curve of the...
register_partition_methodRegister user-defined partition functions
register_top_value_methodRegister user-defined top value methods
remove_partition_methodRemove partition methods
remove_top_value_methodRemove top value methods
run_all_consensus_partition_methodsRun subgroup classification from all methods
select_partition_number-ConsensusPartition-methodSeveral plots for determining the optimized number of...
show-ConsensusPartitionList-methodPrint the ConsensusPartitionList object
show-ConsensusPartition-methodPrint the ConsensusPartition object
show-dispatchMethod dispatch page for show
show-HierarchicalPartition-methodPrint the HierarchicalPartition object
submit_to_davidDoing DAVID analysis
test_between_factorsTest whether a list of factors are correlated
test_to_known_factors-ConsensusPartitionList-methodTest correspondance between predicted and known classes
test_to_known_factors-ConsensusPartition-methodTest correspondance between predicted and known classes
test_to_known_factors-dispatchMethod dispatch page for test_to_known_factors
test_to_known_factors-HierarchicalPartition-methodTest correspondance between predicted and known classes
top_rows_heatmap-ConsensusPartitionList-methodHeatmap of top rows from different top value methods
top_rows_heatmap-dispatchMethod dispatch page for top_rows_heatmap
top_rows_heatmap-matrix-methodHeatmap of top rows from different top methods
top_rows_overlap-ConsensusPartitionList-methodOverlap of top rows from different top value methods
top_rows_overlap-dispatchMethod dispatch page for top_rows_overlap
top_rows_overlap-list-methodOverlap of top rows from different top value methods
top_rows_overlap-matrix-methodOverlap of top rows from different top value methods
venn_eulerMake Venn Euler diagram from a list
jokergoo/cola documentation built on June 27, 2018, 10:35 a.m.