geneOntologyEnrichment {KnowSeq} | R Documentation

## geneOntologyEnrichment obtains the information about what Gene Ontology terms are related to the DEGs.

### Description

The function obtains the information about GO terms from the three differents ontologies that are related to the DEGs. The function also returns the description about each GO and a list of genes that are inside of each GO.

### Usage

    geneOntologyEnrichment(
      geneList,
      geneType = "ENTREZ_GENE_ID",
      ontologies = c("BP", "CC", "MF"),
      pvalCutOff = 1
    )

### Arguments

`geneList` | A list that contains entrez gene id of the DEGs. Entrez gene id can be obtained using getAnnotationFromEnsembl function.
`geneType` | A string indicating the type of genes in geneList, it must be one of indicated in DAVIDs API documentation.
`ontologies` | A list that contains ontologies to be searchs. Values must be contained in the following three: BP, CC, MF.
`pvalCutOff` | The maximum p-value to considers that a genes is related with a GO term.

### Value

A list that contains a matrix for each of the possible ontologies and a matrix with the GOs for the three ontologies together.

### Examples

    ## Not run: GOsList <- geneOntologyEnrichment(data$entrezgene_id,geneType='ENTREZ_GENE_ID',pvalCutOff=0.1)

[Package KnowSeq version 1.2.2 Index]