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]