## ----------------------------------------------------------------------------- exprMatr <- matrix(sample(1:10, 100, replace=TRUE), nrow=20) rownames(exprMatr) <- paste("Gene", 1:20, sep="") colnames(exprMatr) <- paste("Sample", 1:5, sep="") head(exprMatr) ## ----------------------------------------------------------------------------- library(GENIE3) set.seed(123) # For reproducibility of results weightMat <- GENIE3(exprMatr) ## ----------------------------------------------------------------------------- dim(weightMat) weightMat[1:5,1:5] ## ----------------------------------------------------------------------------- # Genes that are used as candidate regulators regulators <- c(2, 4, 7) # Or alternatively: regulators <- c("Gene2", "Gene4", "Gene7") weightMat <- GENIE3(exprMatr, regulators=regulators) ## ----------------------------------------------------------------------------- regulatorsList <- list("Gene1"=rownames(exprMatr)[1:10], "Gene2"=rownames(exprMatr)[10:20], "Gene20"=rownames(exprMatr)[15:20]) set.seed(123) weightList <- GENIE3(exprMatr, nCores=1, targets=names(regulatorsList), regulators=regulatorsList, returnMatrix=FALSE) ## ----eval=FALSE--------------------------------------------------------------- # # Use Extra-Trees (ET) method # # 7 randomly chosen candidate regulators at each node of a tree # # 5 trees per ensemble # weightMat <- GENIE3(exprMatr, treeMethod="ET", K=7, nTrees=50) ## ----eval=FALSE--------------------------------------------------------------- # set.seed(123) # For reproducibility of results # weightMat <- GENIE3(exprMatr, nCores=4, verbose=TRUE) ## ----------------------------------------------------------------------------- ?GENIE3 ## ----------------------------------------------------------------------------- linkList <- getLinkList(weightMat) dim(linkList) head(linkList) ## ----eval=FALSE--------------------------------------------------------------- # linkList <- getLinkList(weightMat, reportMax=5) ## ----eval=FALSE--------------------------------------------------------------- # linkList <- getLinkList(weightMat, threshold=0.1)