--- a
+++ b/man/get_grn.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_grn.R
+\name{get_grn}
+\alias{get_grn}
+\title{Gene Regulatory Network}
+\usage{
+get_grn(X, cluster = NULL, method = c("aracne"), type = "gene")
+}
+\arguments{
+\item{X}{a \code{data.frame}/\code{matrix} with gene expression
+(genes in columns, samples in rows).}
+
+\item{cluster}{(optional) clustering result from
+\code{\link[timeOmics]{getCluster}}}
+
+\item{method}{network building method, one of c('aracne')}
+
+\item{type}{character added to node metadata}
+}
+\value{
+An igraph object if no cluster informations are given.
+Otherwise, it returns a list of igraph object (\code{list.igraph}) with
+a subgraph for each cluster and a global graph with all the genes.
+}
+\description{
+Get Gene Regulatory Network (GRN) from a data.frame.
+Optionally, if the gene are clustered, sub_network are build for
+each cluster.
+}
+\details{
+Methods of GRN reconstruction are as follows:
+'aracne': use ARACNe algorithm on Mutual Information (MI) adjency matrix
+to remove low MI edges in triangles.
+}
+\examples{
+data(hmp_T2D)
+# grn only on gene
+cluster.mRNA <- timeOmics::getCluster(hmp_T2D$getCluster.res, 
+                                      user.block = 'RNA')
+X <- hmp_T2D$raw$RNA
+grn.res <- get_grn(X = hmp_T2D$raw$RNA, 
+                   cluster = cluster.mRNA, 
+                   method = 'aracne')
+
+
+}
+\seealso{
+\code{\link[minet]{build.mim}},
+\code{\link[minet]{aracne}},
+\code{\link[timeOmics]{getCluster}}
+}