ConsensusPartition-class {cola} | R Documentation

## The ConsensusPartition class

### Description

The ConsensusPartition class

### Methods

The `ConsensusPartition-class` has following methods:

`consensus_partition`:

  constructor method, run consensus partition with a specified top-value method and a partition method.

`select_partition_number,ConsensusPartition-method`:

  make a list of plots to select optimized number of partitions.

`consensus_heatmap,ConsensusPartition-method`:

  make heatmap of the consensus matrix.

`membership_heatmap,ConsensusPartition-method`:

  make heatmap of the membership in every random sampling.

`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 partitions.

`collect_classes,ConsensusPartition-method`:

  make heatmap of classes with different numbers of partitions.

`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 in random samplings.

`get_stats,ConsensusPartition-method`:

  get metrics for the consensus clustering.

`get_classes,ConsensusPartition-method`:

  get the consensus class IDs and other columns.

`suggest_best_k,ConsensusPartition-method`:

  guess the best number of partitions.

`test_to_known_factors,ConsensusPartition-method`:

  test correlation between predicted classes and known factors, if available.

`cola_report,ConsensusPartition-method`:

  generate a HTML report for the whole analysis.

`GO_enrichment,ConsensusPartition-method`:

  perform GO enrichment analysis on significant genes if rows in the matrix can be corresponded to genes.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    # There is no example
    NULL

[Package cola version 1.0.1 Index]