gseaData-class {phenoTest} | R Documentation

## Class "gseaData"

### Description

This class is an ES (enrichment score) and ES.sim (simulated enrichment score) container that will be used in the GSEA (Gene Set Enrichment Analysis) process. There is one container for every gene signature.

### Objects from the Class

Objects can be created by calls of the form `new("gseaData", ...)`.

### Slots

`.Data`:

  Object of class `"list"` .

`gseaSignaturesSign`:

  Object of class `"gseaSignaturesSign"` or `"gseaSignaturesVar"`.

`gseaSignificanceSign`:

  Object of class `"gseaSignificanceSign"` or `"gseaSignificanceVar"`.

### Extends

Class `"list"`, from data part. Class `"vector"`, by class "list", distance 2. Class `"AssayData"`, by class "list", distance 2.

### Methods

getEs

  `signature(x = "gseaData")`: Returns the enrichment scores.

getEsSim

  `signature(x = "gseaData")`: Returns the simulated enrichemt scores (the ones obtained after permutations).

getFcHr

  `signature(x = "gseaData")`: Returns the fold change and/or the hazard ratio that were used to compute the enrichment scores.

### Author(s)

Evarist Planet

### Examples

    showClass("gseaSignaturesSign")

[Package phenoTest version 1.35.1 Index]