GRN {MoonlightR} | R Documentation

## Generate network

### Description

This function carries out the gene regulatory network inference using parmigene

### Usage

    GRN(TFs, DEGsmatrix, DiffGenes = FALSE, normCounts, kNearest = 3,
      nGenesPerm = 10, nBoot = 10, seed = 12345)

### Arguments

`TFs` | a vector of genes.
`DEGsmatrix` | DEGsmatrix output from DEA such as dataDEGs
`DiffGenes` | if TRUE consider only diff.expr genes in GRN
`normCounts` | is a matrix of gene expression with genes in rows and samples in columns.
`kNearest` | the number of nearest neighbors to consider to estimate the mutual information.
`nGenesPerm` | nGenesPerm
`nBoot` | nBoot
`seed` | set to get same result Must be less than the number of columns of normCounts.

### Value

an adjacent matrix

### Examples

    dataDEGs <- DEGsmatrix
    dataGRN <- GRN(TFs = rownames(dataDEGs)[1:100],
    DEGsmatrix = dataDEGs,
    DiffGenes = TRUE,
    normCounts = dataFilt)

[Package MoonlightR version 1.8.0 Index]