GEVACluster-class {geva} | R Documentation

## GEVA Clustering Results

### Description

The `GEVACluster` class represents the classification results from a cluster analysis. For each probe/gene, there is a assigned cluster among the g defined clusters.

This class inherits from `GEVAGroupSet`.

### Value

A `GEVACluster` object

### Slots

`grouping`

  `factor` (m elements, g levels), cluster assignment for each gene/probe
  (Inherited from `GEVAGroupSet`)

`scores`

  `numeric` vector (m elements) comprising a score value for each cluster assignment
  (Inherited from `GEVAGroupSet`)

`ftable`

  `data.frame` (m lines) with additional cluster assignment features
  (Inherited from `GEVAGroupSet`)

`centroids`

  `numeric SVTable` (g lines) with the S and V centroid coordinates for each cluster
  (Inherited from `GEVAGroupSet`)

`offsets`

  `numeric SVTable` (m lines) with the S and V coordinate offsets each gene/probe from its cluster centroid
  (Inherited from `GEVAGroupSet`)

`info`

  `list` of supplementary information
  (Inherited from `GEVAGroupSet`)

`cluster.method`

  `character`, method used in the cluster analysis (see `geva.cluster`)

### Methods

(See also the inherited methods from `GEVAGroupSet`)

Plotting

`lines(x, ...)`

  Draws convex hulls around the clustered points

`plot(x, y, ...)`

  Draws a SV-plot that highlights the clustered points. Convex hulls are included for visual purposes only and do not avoid enclosing points from other clusters on concave parts.
  Can be combined with another `SVTable` or `GEVAGroupSet` given as the `y` argument to include additional graphical elements

[Package geva version 1.2.0 Index]