GEVAGroupSet-class {geva} | R Documentation

## GEVA Grouping Results

### Description

The `GEVAGroupSet` class represents the classification of summarized values from a `SVTable`, where each gene/probe has one assigned group among `g` defined groups. This is an abstract class. Inherits the `GEVACluster` and `GEVAQuantiles` classes.

### Value

A `GEVAGroupSet` object

### Slots

`grouping`

  `factor` (m elements, g levels) used to group the genes/probes

`scores`

  `numeric` vector (m elements) with the assigned grouping scores for each gene/probe

`ftable`

  `data.frame` (m lines) with additional grouping features

`centroids`

  `numeric SVTable` (g lines) with the S and V centroid coordinates for each group

`offsets`

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

`info`

  `list` of additional information

### Methods

Alternative accessors

`levels(x)`

  Returns the unique group names included in the group set.
  Equivalent to `levels(groups(x))`

Conversion and coercion

`as.data.frame(x, row.names = names(x), ...)`

  Returns a `data.frame` with the `groups` and `scores` slots as columns

`as.expression(x, sv, ...)`

  Gets the expression that reproduces this `GEVAGroupSet` object, including function parameters used by `geva.cluster`. The `sv` argument is optional but can be specified to replace the source `SVTable`

`as.SVTable(x, which = c("sv", "offsets", "centroids"), ...)`

  Retrieves a `SVTable` based on the contents indicated by `which`. The accepted arguments are: `sv` for the source data; `offsets` for the `offsets` slots; and `centroids` for the `centroids` slot

Dimension accessors

`length(x)`

  Returns the number of rows in the `sv` slot

`names(x)`

  Gets the assigned names by the classification and scores

Plotting

`color.values(x, point.col = NULL, ...)`

  Gets the colors associated to the grouped data points. If not present, generates random group colors.
  If `point.col` is a single `character` or an vector of the same length of data points, adjusts the color values to web RGBA

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

  Draws a SV-plot that highlights the grouped information.
  Can be combined with another `SVTable` or `GEVAGroupSet` given as the `y` argument to include additional graphical elements

`points(x, ...)`

  Draws the grouped points

Properties

`analysis.params(gobject)`

  Returns a `list` of analysis parameters passed to `geva.cluster` to obtain this object

`cluster.method(object)`

  Returns the option used as the `cluster.method` argument when calling `geva.cluster`

Sub-slot accessors

`classification.table(object) <- value`

  Stores the classification `data.frame` on this object

`classification.table(object)`

  Returns a `data.frame` of predicted classifications, if supported by this object

`sv.data(object)`

  Returns a `SVTable` with the source SV coordinates

`sv(object)`

  Returns the `numeric matrix` in the `SVTable` from `sv.data(object)`

[Package geva version 1.2.0 Index]