HierarchicalPartition-class {cola} | R Documentation

## The HierarchicalPartition class

### Description

The HierarchicalPartition class

### Methods

The `HierarchicalPartition-class` has following methods:

`hierarchical_partition`:

  constructor method.

`collect_classes,HierarchicalPartition-method`:

  plot the hierarchy of subgroups predicted.

`get_classes,HierarchicalPartition-method`:

  get the class IDs of subgroups.

`suggest_best_k,HierarchicalPartition-method`:

  guess the best number of partitions for each node.

`get_matrix,HierarchicalPartition-method`:

  get the original matrix.

`get_signatures,HierarchicalPartition-method`:

  get the signatures for each subgroup.

`dimension_reduction,HierarchicalPartition-method`:

  make dimension reduction plots.

`test_to_known_factors,HierarchicalPartition-method`:

  test correlation between predicted subgrouping and known annotations, if available.

`cola_report,HierarchicalPartition-method`:

  generate a HTML report for the whole analysis.

`GO_enrichment,HierarchicalPartition-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]