--- a
+++ b/geneGO2.R
@@ -0,0 +1,47 @@
+library(topGO)
+library(limma)
+library(edgeR)
+library(org.Hs.eg.db)
+
+data = read.table("lung.txt", header = T, sep = "\t")
+data2 = data[data$X != "SLC35E2",]
+rownames(data2) = data2[,1]
+data = data2[,-1]
+condition = factor(rep(c("T1", "T2"), c(576, 552)))
+design = model.matrix(~condition)
+
+dge = DGEList(counts=as.matrix(data), group = condition)
+dge = calcNormFactors(dge, method = "TMM") #webtool'da var. RLE dediği deseq, TMM dediği TMM, none dediği none
+v = voom(dge,design,plot=F) 
+fit = lmFit(v,design)
+fit = eBayes(fit)
+res = topTable(fit,coef=ncol(design),number = dim(data)[1])
+geneList = res$adj.P.Val #voomNSC tarafından seçilen genler
+names(geneList) = rownames(res) #voomNSC tarafından seçilen genler
+biomarkers = rownames(res[10:50,]) #voomNSC tarafından seçilen genler
+#truefalse = is.element(names(geneList),biomarkers)
+#selection = function(x) TRUE 
+
+#allGO2genes = annFUN.org(whichOnto='BP', feasibleGenes = NULL,
+#                         mapping="org.Hs.eg.db", ID = "genename")
+
+#GOdata = new("topGOdata", description = "Simple session", ontology = "BP",
+# allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10,
+# annot = annFUN.db, affyLib = affyLib)
+truefalse = function(allScore) {  
+  truefalse = is.element(names(geneList),biomarkers)
+  return(truefalse)
+}
+
+allGO2genes = annFUN.org(whichOnto='BP', feasibleGenes = NULL,
+                         mapping="org.Hs.eg.db", ID = "symbol")
+GOdata =  new('topGOdata', ontology = 'BP', allGenes = geneList, 
+              annot = annFUN.GO2genes, GO2genes = allGO2genes, 
+              geneSel = truefalse, nodeSize=10)
+
+results.ks = runTest(GOdata, algorithm = "classic", statistic = "ks")
+results.ks
+allRes = GenTable(GOdata, KS = results.ks, orderBy = "KS", topNodes = 20)
+allRes[,c('GO.ID','Term','KS')]
+showSigOfNodes(GOdata, score(results.ks), firstSigNodes = 5, useInfo = 'all')
+