GRN: Generate network

View source: R/GRN.R

GRNR 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
)

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. Must be less than the number of columns of normCounts.

nGenesPerm

nGenesPerm

nBoot

nBoot

Value

an adjacent matrix

Examples

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

ibsquare/MoonlightR documentation built on May 19, 2024, 6:16 a.m.