geneOntologyEnrichment {KnowSeq} | R Documentation |
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.
geneOntologyEnrichment(geneMatrix, labels, identificator = "SYMBOL", mapping = "org.Hs.eg.db", nGOs = 10, pvalCutOff = 0.01)
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. |
A list that contains a matrix for each of the possible ontologies and a matrix with the GOs for the three ontologies together.
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)