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TopGO_manual .md

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GO enrichment using TopGO

Written by Gamaliel López-Leal

gamaliel.lopez@uaem.edu.com

 library ("topGO")
 library ("Rgraphviz")

Read your gene background or GO universe

geneID2GO <- readMappings(file = "MG_GO_universe.txt" , sep = "\t", IDsep = ",")

geneNames <- names(geneID2GO)

geneUniverse <- names(geneID2GO)

Read your gene list of interest

genesOfInterest <- read.table("Chicken_Chicken-Breeders.txt",header=FALSE)

genesOfInterest <- as.character(genesOfInterest$V1)

geneList <- factor(as.integer(geneUniverse %in% genesOfInterest))

names(geneList) <- geneUniverse

Build the TopGO annotation set

myGOdata <- new("topGOdata", ontology="MF", allGenes=geneList,  annot = annFUN.gene2GO, gene2GO = geneID2GO)

Run the GO enrichment

resultTopgo <- runTest(myGOdata, algorithm="classic", statistic="fisher")

Make gene table with the GO enrichment results

allResTopGO2 <- GenTable(myGOdata, topgoFisher = resultTopgo, ranksOf = "classicFisher", topNodes = 100)

Plot the results

showSigOfNodes(myGOdata, score(resultTopgo), firstSigNodes = 5, useInfo = 'all')