GRN: Generate network

In ibsquare/MoonlightR: Identify oncogenes and tumor suppressor genes from omics data

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 Aug. 21, 2023, 7:16 a.m.