gseaSignaturesSign-class: Class "gseaSignaturesSign"

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 gene signature.

Objects from the Class

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

Slots

.Data:

Object of class "list" .

gseaSignatures:

Object of class "gseaSignatures" This is the object that will contain the ES and ES.sim.

es.sim.gam:

Object of class "matrix" enrichment scores computed with the gam method.

fc.hr:

Object of class "character" fold change or hazard ratio used to compute the enrichment scores.

s:

Object of class "logical" The subset of genes we are interested in.

test:

Object of class "character" The statistical test that will be used.

Extends

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

Methods

getEs

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

getEsSim

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

getFcHr

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

gseaSignificance

signature(x = "gseaSignaturesSign"): 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("gseaSignaturesSign")

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