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

ConsensusPartition-class

R Documentation

The ConsensusPartition class

Description

The ConsensusPartition class

Methods

The ConsensusPartition-class has following methods:

consensus_partition:: constructor method, run consensus partitioning with a specified top-value method and a partitioning method.
select_partition_number,ConsensusPartition-method:: make a list of plots for selecting optimized number of subgroups.
consensus_heatmap,ConsensusPartition-method:: make heatmap of the consensus matrix.
membership_heatmap,ConsensusPartition-method:: make heatmap of the membership for individual partitions.
get_signatures,ConsensusPartition-method:: get the signature rows and make heatmap.
dimension_reduction,ConsensusPartition-method:: make dimension reduction plots.
collect_plots,ConsensusPartition-method:: make heatmaps for consensus matrix and membership matrix with different number of subgroups.
collect_classes,ConsensusPartition-method:: make heatmap with subgroups with different numbers.
get_param,ConsensusPartition-method:: get parameters for the consensus clustering.
get_matrix,ConsensusPartition-method:: get the original matrix.
get_consensus,ConsensusPartition-method:: get the consensus matrix.
get_membership,ConsensusPartition-method:: get the membership of partitions generated from random samplings.
get_stats,ConsensusPartition-method:: get statistics for the consensus partitioning.
get_classes,ConsensusPartition-method:: get the consensus subgroup labels and other columns.
suggest_best_k,ConsensusPartition-method:: guess the best number of subgroups.
test_to_known_factors,ConsensusPartition-method:: test correlation between predicted subgroups and known factors, if available.
cola_report,ConsensusPartition-method:: generate a HTML report for the whole analysis.
functional_enrichment,ConsensusPartition-method:: perform functional enrichment analysis on significant genes if rows in the matrix can be corresponded to genes.