This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data. https://bioconductor.org/packages/release/bioc/vignettes/GENIE3/inst/doc/GENIE3.html#obtain-more-information-1
1.GENIE3 {GENIE3}.GENIE3 Infers a gene regulatory network (in the form of a weighted adjacency matrix) from expression data, using ensembles of regression trees.
library(GENIE3)
## Generate fake expression matrix
exprMatrix <- matrix(sample(1:10, 100, replace=TRUE), nrow=20)
rownames(exprMatrix) <- paste("Gene", 1:20, sep="")
colnames(exprMatrix) <- paste("Sample", 1:5, sep="")
## Run GENIE3
set.seed(123) # For reproducibility of results
weightMatrix <- GENIE3(exprMatrix, regulators=paste("Gene", 1:5, sep=""))
## Get ranking of edges
linkList <- getLinkList(weightMatrix)
head(linkList)## regulatoryGene targetGene weight
## 1 Gene4 Gene1 0.6256487
## 2 Gene3 Gene2 0.5983628
## 3 Gene3 Gene4 0.5297676
## 4 Gene2 Gene17 0.5031615
## 5 Gene5 Gene8 0.4877041
## 6 Gene3 Gene10 0.4403217## Different regulators for each gene & return as list
regulatorsList <- list("Gene1"=rownames(exprMatrix)[1:10],
"Gene2"=rownames(exprMatrix)[10:20],
"Gene20"=rownames(exprMatrix)[15:20])
set.seed(123)
weightList <- GENIE3(exprMatrix, nCores=1, targets=names(regulatorsList), regulators=regulatorsList, returnMatrix=FALSE)2.getLinkList {GENIE3}.getLinkList Converts the weight matrix, as returned by GENIE3, to a sorted list of regulatory links (most likely links first).
## Generate fake expression matrix
exprMat <- matrix(sample(1:10, 100, replace=TRUE), nrow=20)
rownames(exprMat) <- paste("Gene", 1:20, sep="")
colnames(exprMat) <- paste("Sample", 1:5, sep="")
## Run GENIE3
weightMat <- GENIE3(exprMat, regulators=paste("Gene", 1:5, sep=""))
## Get ranking of edges
linkList <- getLinkList(weightMat)
head(linkList)## regulatoryGene targetGene weight
## 1 Gene1 Gene8 0.5723736
## 2 Gene2 Gene4 0.5013760
## 3 Gene5 Gene13 0.4994663
## 4 Gene4 Gene17 0.4895139
## 5 Gene2 Gene5 0.4552329
## 6 Gene4 Gene20 0.4476125This package is deprecated. It will probably be removed from Bioconductor.
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