ConsensusPartitionList-class: The ConsensusPartitionList class
In jokergoo/cola: A Framework for Consensus Partitioning

ConsensusPartitionList-class

R Documentation

The ConsensusPartitionList class

Description

The ConsensusPartitionList class

Details

The object contains results from all combinations of top-value methods and partitioning methods.

Methods

The ConsensusPartitionList-class provides following methods:

run_all_consensus_partition_methods:: constructor method.
top_rows_overlap,ConsensusPartitionList-method:: plot the overlaps of top rows under different top-value methods.
top_rows_heatmap,ConsensusPartitionList-method:: plot the heatmap of top rows under different top-value methods.
get_classes,ConsensusPartitionList-method:: get consensus subgroup labels merged from all methods.
get_matrix,ConsensusPartition-method:: get the original matrix.
get_stats,ConsensusPartitionList-method:: get statistics for the partition for a specified k.
get_membership,ConsensusPartitionList-method:: get consensus membership matrix summarized from all methods.
suggest_best_k,ConsensusPartitionList-method:: guess the best number of subgroups for all methods.
collect_plots,ConsensusPartitionList-method:: collect plots from all combinations of top-value methods and partitioning methods with choosing a plotting function.
collect_classes,ConsensusPartitionList-method:: make a plot which contains predicted subgroups from all combinations of top-value methods and partitioning methods.
test_to_known_factors,ConsensusPartitionList-method:: test correlation between predicted subgroups and known annotations, if provided.
cola_report,ConsensusPartitionList-method:: generate a HTML report for the whole analysis.
functional_enrichment,ConsensusPartitionList-method:: perform functional enrichment analysis on significant genes if rows in the matrix can be corresponded to genes.