GEVAQuantiles-class {geva} | R Documentation

## GEVA Quantiles Grouping Results

### Description

The `GEVAQuantiles` class represents the results of a quantile detection analysis. For each probe/gene, there is a assigned quantile among the g defined quantiles.

This class inherits from `GEVAGroupSet` and is inherited by `GEVAQuantilesAdjusted`.

### Value

A `GEVAQuantiles` object

### Slots

`grouping`

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

`scores`

  `numeric` vector (m elements) with the assigned quantile scores for each gene/probe
  (Inherited from `GEVAGroupSet`)

`ftable`

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

`centroids`

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

`offsets`

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

`info`

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

`svscores`

  `numeric SVTable` (m lines) with individual partial scores for the assigned quantiles

`qareasizes`

  `numeric SVTable` (g lines) with the S and V sizes for each quantile

`qindexes`

  `integer SVTable` (g lines) representing the position index to each quantile, in terms of summary and variation

`qcount`

  integer attributes (`SVIntAttribute`) with the defined number of quantiles for the S and V axes

`qcutoff`

  numeric attributes (`SVNumAttribute`) with the initial quantile cutoff in S and V, starting from the point zero

`qmethod`

  `character`, method used to calculate the initial quantiles (see `geva.quantiles()`)

### Methods

(See also the inherited methods from `GEVAGroupSet`)

Conversion and coercion

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

  Converts this object to `expression`

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

  Converts this object to `SVTable`

Plotting

`lines(x, ...)`

  Draws the quantile delimiter lines

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

  Draws a SV-plot that highlights the points from each quantile. Dashed lines are included as the quantile delimiters.
  Can be combined with another `SVTable` or `GEVAGroupSet` given as the `y` argument to include additional graphical elements

Properties

`cluster.method(object)`

  Returns the option used as the `cluster.method` argument when calling `geva.cluster`.
  Instances of this object always return `'quantiles'`

Sub-slot accessors

`classification.table(object) <- value`

  Sets the `data.frame` with the qualitative contrasts of classification relevance

`classification.table(object)`

  Gets a `data.frame` with the qualitative contrasts of classification relevance

`quantiles(object)`

  Gets the unique quantile names

[Package geva version 1.0.0 Index]