% 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}}

}