geneOntologyEnrichment: geneOntologyEnrichment obtains the information about what...

In CasedUgr/KnowSeq: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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)

CasedUgr/KnowSeq documentation built on Aug. 16, 2022, 6:19 a.m.