getLinkList: getLinkList

In GENIE3: GEne Network Inference with Ensemble of trees

Description

getLinkList Converts the weight matrix, as returned by GENIE3, to a sorted list of regulatory links (most likely links first).

Usage

getLinkList(weightMatrix, reportMax = NULL, threshold = 0)

Arguments

weightMatrix	Weighted adjacency matrix as returned by GENIE3.
reportMax	Maximum number of links to report. The default value NULL means that all the links are reported.
threshold	Only links with a weight equal or above the threshold are reported. Default: threshold = 0, i.e. all the links are reported.

Value

List of regulatory links in a data frame. Each line of the data frame corresponds to a link. The first column is the regulatory gene, the second column is the target gene, and the third column is the weight of the link.

See Also

GENIE3

Examples

## 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)

GENIE3 documentation built on Nov. 8, 2020, 5:52 p.m.