geneOntologyEnrichment: geneOntologyEnrichment obtains the information about what...

Description Usage Arguments Value Examples

View source: R/geneOntologyEnrichment.R

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

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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

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

KnowSeq documentation built on April 16, 2021, 6:01 p.m.