getLinkList: getLinkList

Description Usage Arguments Value See Also Examples

View source: R/getLinkList.R

Description

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

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
## 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.