GEVAResults-class {geva} | R Documentation

## GEVA Results Table

### Description

The `GEVAResults` class contains the final results from GEVA analyses. It represents the results of multiple statistical approaches from summary/variation data, clustering, quantile detection, and factor analysis (if applicable).

### Value

A `GEVAResults` object

### Slots

`resultstable`

  `data.frame` (m lines) with classification results for the genes/probes

`svdata`

  `GEVASummary` used as input

`quantdata`

  `GEVAQuantiles` or `GEVAQuantilesAdjusted` with the final quantile assignments for the summarized data

`factoring`

  `data.frame` (m lines) with detailed results for the factor analyses, such as p-values for each factor. If there was no factor analysis, this slot is `NULL` or empty

`classiftable`

  `data.frame` used as reference for the final classification

`info`

  `list` of supplementary information

### Methods

Conversion and coercion

`as.expression(x, gsummary, gquants, ...)`

  Gets the expression that reproduces this `GEVAResults` object, including function parameters used by `geva.finalize`. The `gsummary` and `gquants` arguments are optional but can be specified to replace the internal `GEVASummary` and `GEVAQuantiles`, respectively

Dimension accessors

`dim(x)`

  Returns the dimensions from the `resultstable` slot

`dimnames(x)`

  Returns a `list` with the row and column names from the `results.table` slot.
  Individual dimension names can also be accessed through `rownames` and `colnames`

`length(x)`

  Returns the number of rows in the `resultstable` slot

`names(x)`

  Returns the column names from the `resultstable` slot

Plotting

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

  Draws a SV-plot that highlights the relevant points from adjusted quantiles

`points(x, which, ..., classif)`

  Draws the results points.
  If `which` (`character` vector) is given, plots only the matching genes/probes.
  If `classif` (`character` vector) is given, plots only points with the matching classification

Properties

`x$name <- value`

  Extracts a column from the `resultstable` slot

`x[i, j, ..., drop=TRUE]`

  Extracts the contents from the `resultstable` slot

`analysis.params(gobject)`

  Returns a `list` of analysis parameters passed to `geva.finalize` or `geva.quick` to obtain this object

Sub-slot accessors

`featureTable(object)`

  Returns the features `data.frame` from the internal `GEVAInput`

`head(x, ...)`

  Returns the first lines of `results.table(x)`

`inputdata(object)`

  Returns the internal `GEVAInput`

`inputvalues(object)`

  Returns the values `matrix` from the internal `GEVAInput`

`inputweights(object, normalized)`

  Returns the weights `matrix` from the internal `GEVAInput`

`levels(x)`

  Returns the factors used in factor analysis, if present

[Package geva version 1.0.0 Index]