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HerwigAppendix-1.txt

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+Appendix 1 � R-code
+
+
+
+
+#Normalization
+
+
+library(gcrma)
+
+#in the following line, replace CEL directory and CDF name with respective folder and name of your custom CDF
+
+set <- ReadAffy(celfile.path=<CEL directory>, cdfname = <custom CDF name>)
+
+nset <- gcrma(set)
+
+
+
+
+#Differential expression
+
+
+library(limma)
+
+design <- model.matrix(~ 0+factor(c(1,1,2,2))) 
+
+# exemplary design matrix for the case that samples 1 and 2 are control, 3 and 4 are treatment; adjust accordingly
+
+fit <- lmFit(nset, design)
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+fit <- eBayes(fit)
+
+topTable(fit)
+
+
+
+
+#Induced network modules
+
+
+library(BioNet)
+
+#in the following line, replace PPI file with the file name of the PPI in standard interaction format (.sif)
+
+ppi <- read.csv(<PPI file in sif>, sep="\t", header=T)
+
+ppiG <- ftM2graphNEL(ppi, edgemode="undirected")
+
+#in the following line, replace diffEx file with the table acuired in Method 3.1.2 step 5
+
+deData <- read.csv(<diffEx file>, sep="\t", header=T)
+
+subnet <- subNetwork(deData$Gene.ID, ppiG)
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+fb <- fitBumModel(pval, plot = FALSE)	
+
+#pval = 0.05, for example
+
+scores <- scoreNodes(subnet, fb, fdr = 0.01)	
+
+#play around with the fdr value to acquire modules of interpretable size
+
+module <- runFastHeinz(subnet, scores)
+
+plotModule(module, scores = scores, diff.expr = logFC)
+