Man pages for jokergoo/cola
Unsupervised subgroup classification based on consensus clustering

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 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
collect_classes-ConsensusPartitionList-methodCollect classes from ConsensusPartitionList object
collect_classes-ConsensusPartition-methodCollect classes from ConsensusPartitionList 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
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 columns 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
get_best_k-ConsensusPartitionList-methodGet the best number of partitions
get_best_k-ConsensusPartition-methodGet the best number of partitions
get_best_k-dispatchMethod dispatch page for get_best_k
get_class-ConsensusPartitionList-methodGet class from the ConsensusPartitionList object
get_class-ConsensusPartition-methodGet class from the ConsensusPartition object
get_class-dispatchMethod dispatch page for get_class
get_class-HierarchicalPartition-methodGet class from the HierarchicalPartition object
get_consensus-ConsensusPartition-methodGet consensus matrix
get_membership-ConsensusPartition-methodGet membership matrix
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_single_run-ConsensusPartitionList-methodGet result for a single top method and partition method
get_single_run-dispatchMethod dispatch page for get_single_run
get_single_run-HierarchicalPartition-methodGet result for a specified level in the partition hierarchy
get_stat-ConsensusPartitionList-methodGet statistics
get_stat-ConsensusPartition-methodGet statistics
get_stat-dispatchMethod dispatch page for get_stat
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 columns in each random sampling
PACPAC score
plot_ecdf-ConsensusPartition-methodPlot the ecdf of the consensus matrix
reduce_david_resultsReduce DAVID results
register_partition_funRegister user-defined partition functions
register_top_value_funRegister user-defined top value functions
remove_partition_methodRemove partition methods
remove_top_value_methodRemove top 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
signature_density-ConsensusPartition-methodDensity for the signatures
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 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 methods
top_rows_overlap-dispatchMethod dispatch page for top_rows_overlap
top_rows_overlap-list-methodOverlap of top rows from different top methods
top_rows_overlap-matrix-methodOverlap of top rows from different top methods
venn_eulerMake Venn Euler diagram from a list
jokergoo/cola documentation built on Jan. 8, 2018, 6:24 p.m.