% 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}}
}