neominitutorial.docVIP

NEO Mini Tutorial Jason Aten, Steve Horvath Here we describe the basic commands and output of the network edge orienting software (NEO) using a simple example. We simulate two expression traits E1 and E2 and anchor them to two SNP markers each. Next we compute edge orienting scores for evaluating the orientation E1 - E2. If you are interested in a simulated example involving multiple traits and edges, we recommend another NEO tutorial called NEOTutorialMultiEdgeSimulation.doc. To cite this tutorial and the R code, please use the following reference. Aten JE, Fuller TF, Lusis AJ, Horvath S (2008) Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Systems Biology 2008, 2:34 # Copy and paste the following functions into R # The following path should be rather small. A long pathy may result in an error. dir.create(C:/NEOminiTutorial) setwd(C:/NEOminiTutorial) # Please adapt the following paths so that the point to the directory where # the causality function files are located. Note that we use / instead of \ source(C:/Documents and Settings/Steve Horvath/My Documents/RFunctions/CausalityFunctions.txt) source(C:/Documents and Settings/Steve Horvath/My Documents/RFunctions/updatedneo.txt) # this is the number of samples (e.g. number of mice or humans) no.samples=100 # Here we set the random seed so that the simulation results become reproducible. set.seed(1); # here we simulate SNP markers will allele frequency 0.5. SNP1= sample(c(0,1,2), size=no.samples, prob=c(.25,.5,.25) ,replace=T); SNP2= sample(c(0,1,2), size=no.samples, prob=c(.25,.5,.25) ,replace=T); SNP3= sample(c(0,1,2), size=no.samples, prob=c(.25,.5,.25) ,replace=T); SNP4= sample(c(0,1,2), size=no.samples, prob=c(.25,.5,.25) ,replace=T); environmental.variation=0.5; # SNPs 1 and 2 additively cause variation in E1 E1=scale(scale(SNP1+SNP2)+rnorm(no.samples,sd=sqrt(environmental.variation))) # Now we simulate E1 - E2 and SNPs