epheno-class: Class "epheno"

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

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")

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.