gseaSignaturesVar-class: Class "gseaSignaturesVar"

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

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 phenotype. Every one of this containers (of class gseaSignaturesSign) is a container itsef and has the enrichment scores of all signatures. GseaSignaturesVar contains one element per phenotype (phenotypic variable). Every one of this elements is of class gseaSignaturesSign and contains one element per signature.

Objects from the Class

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

Slots

.Data:

Object of class "list".

gseaSignatures:

Object of class "gseaSignaturesSign" This object contains the enrichment scores and other elements that will be used in the GSEA process.

Extends

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

Methods

getEs

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

getEsSim

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

getFcHr

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

gseaSignificance

signature(x = "gseaSignaturesVar"): This is the next step in the process of performing GSEA. This funtion will test if the gene sets are enriched.

Author(s)

Evarist Planet

Examples

showClass("gseaSignaturesVar")

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