TCGAanalyze_EAcomplete: Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and...

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways

Description

Researchers, in order to better understand the underlying biological processes, often want to retrieve a functional profile of a set of genes that might have an important role. This can be done by performing an enrichment analysis.

We will perform an enrichment analysis on gene sets using the TCGAanalyze_EAcomplete function. Given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find identify classes of genes or proteins that are #'over-represented using annotations for that gene set.

Usage

TCGAanalyze_EAcomplete(TFname, RegulonList)

Arguments

TFname	is the name of the list of genes or TF's regulon.
RegulonList	List of genes such as TF's regulon or DEGs where to find enrichment.

Value

Enrichment analysis GO[BP,MF,CC] and Pathways complete table enriched by genelist.

Examples

Genelist <- c("FN1","COL1A1")
ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist)
## Not run: 
Genelist <- rownames(dataDEGsFiltLevel)
system.time(ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist))

## End(Not run)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.