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(geneMatrix, labels, identificator = "SYMBOL",
  mapping = "org.Hs.eg.db", nGOs = 10, pvalCutOff = 0.01)

Arguments

geneMatrix

A matrix that contains the expression of the DEGs for each samples.

labels

A vector that contains the labels of the samples of the DEGsMatrix.

identificator

The identification methods for the genes. By default the identificator is the gene symbol or gene name.

mapping

The annotation database to map the gene and GOs. By default is prepared for homo sapiens but can be changed for other species.

nGOs

Maximun number of GOs to return of the total amount of top GOs. By default is equal to 10.

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

dir <- system.file("extdata", package="KnowSeq")
load(paste(dir,"/expressionExample.RData",sep = ""))

labelsGo <- gsub("Control",0,labels)
labelsGo <- gsub("Tumor",1,labelsGo)

GOsList <- geneOntologyEnrichment(DEGsMatrix,labelsGo,nGOs = 20,pvalCutOff = 0.001)

[Package KnowSeq version 1.0.0 Index]