ConsensusPartitionList-class {cola} | R Documentation

## The ConsensusPartitionList class

### Description

The ConsensusPartitionList class

### Details

The object contains results from all combinations of top-value methods and partition 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 class IDs merging from all methods.

`get_matrix,ConsensusPartition-method`:

  get the original matrix.

`get_stats,ConsensusPartitionList-method`:

  get metrics 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 partitions for all methods.

`collect_plots,ConsensusPartitionList-method`:

  collect plots from all combinations of top-value methods and partition methods with choosing a plotting function.

`collect_classes,ConsensusPartitionList-method`:

  make a plot which contains predicted classes from all combinations of top-value methods and partition methods.

`test_to_known_factors,ConsensusPartitionList-method`:

  test correlation between predicted classes and known annotations, if provided.

`cola_report,ConsensusPartitionList-method`:

  generate a HTML report for the whole analysis.

`GO_enrichment,ConsensusPartitionList-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>

### See Also

The `ConsensusPartition-class`.

### Examples

    # There is no example
    NULL

[Package cola version 1.0.1 Index]