TCGAanalyze_EAcomplete {TCGAbiolinks} | R Documentation

## 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)

[Package TCGAbiolinks version 2.20.1 Index]