epheno-class {phenoTest} | R Documentation

## Class "epheno"

### Description

Object obtained with the ExpressionPhenoTest function. Contains FC, HR and pvals from testing expression values of each gene against phenotypic variables.

### Objects from the Class

Objects can be created by calls of the form `new("epheno", assayData, phenoData, featureData, exprs, ...)`.

### Slots

`p.adjust.method`:

  Object of class `"character"` containing the multiple testing adjustment method used (if one was used).

`approach`:

  Object of class `"character"` containing 'frequentist' or 'bayesian' depending on the user's selecion.

`assayData`:

  Object of class `"AssayData"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

`phenoData`:

  Object of class `"AnnotatedDataFrame"` that contains information about the variables stored in the experimentData slot such as their class (continuous, categorical, etc) or type (mean, summaryDif, pval, etc).

`featureData`:

  Object of class `"AnnotatedDataFrame"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

`experimentData`:

  Object of class `"MIAME"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

`annotation`:

  Object of class `"character"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

`protocolData`:

  Object of class `"AnnotatedDataFrame"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

`.__classVersion__`:

  Object of class `"Versions"` that is inherited from the `ExpressionSet` object used to create the `epheno` object.

### Extends

Class `"ExpressionSet"`, directly. Class `"eSet"`, by class "ExpressionSet", distance 2. Class `"VersionedBiobase"`, by class "ExpressionSet", distance 3. Class `"Versioned"`, by class "ExpressionSet", distance 4.

### Methods

[

  `signature(x = "epheno", i = "ANY", j = "ANY")`: inherited from the `ExpressionSet` class.

dim

  `signature(x = "epheno")`: inherited from the `ExpressionSet` class.

export2CSV

  `signature(x = "epheno")`: ...

getFc

  `signature(x = "epheno")`: getter for the fold changes.

getHr

  `signature(x = "epheno")`: getter for the hazard ratios.

getMeans

  `signature(x = "epheno")`: getter for the means.

getSignif

  `signature(x = "epheno")`: getter for the pvalues or posterior probabilities.

getPvals

  `signature(x = "epheno")`: getter for the pvalues.

getPostProbs

  `signature(x = "epheno")`: getter for the posterior probabilities.

getSummaryDif

  `signature(x = "epheno")`: getter that returns hazard ratios, fold changes and pvalues.

gseaSignatures

  `signature(x = "epheno", signatures = "list")`: Used to compute GSEA. Please read the gseaSignatures manual.

logFcHr

  `signature(x = "epheno")`: getter for the log of fold changes and hazard ratios.

p.adjust.method

  `signature(x = "epheno")`: getter for the p value adjustment method that has been used.

phenoClass

  `signature(x = "epheno")`: Returns the class off all variables.

phenoNames

  `signature(x = "epheno")`: Returns the names of the tested phenotypes.

show

  `signature(object = "epheno")`: Shows a brief overview of the object.

### Author(s)

Evarist Planet

### Examples

    showClass("epheno")

[Package phenoTest version 1.34.0 Index]