--- a
+++ b/man/compute_gene_network.Rd
@@ -0,0 +1,83 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/layers.R
+\name{compute_gene_network}
+\alias{compute_gene_network}
+\title{Compute gene netwok from scRNA-seq data}
+\usage{
+compute_gene_network(
+  hummus,
+  gene_assay = "RNA",
+  tfs = NULL,
+  method = "GENIE3",
+  multiplex_name = NULL,
+  network_name = NULL,
+  store_network = FALSE,
+  output_file = NULL,
+  threshold = 0,
+  number_cores = 1,
+  verbose = 1
+)
+}
+\arguments{
+\item{hummus}{(Hummus_Object) - Hummus object}
+
+\item{gene_assay}{(character) - Name of the assay containing the gene
+expression data.}
+
+\item{tfs}{vector(character) - List of tfs considered. If NULL, all TFs with
+motifs in the hummus object are used.}
+
+\item{method}{(character) - Method used to infer network edges.
+\itemize{
+\item \code{'Genie3'} - Use tree random forest to infer regulatory networks.
+\item \code{'Other method'} - TO DO.
+}}
+
+\item{multiplex_name}{(character) - Name of the multiplex to add the network
+to. Default is \code{'RNA'}.}
+
+\item{network_name}{(character) - Name of the network in the multiplex to
+add the network to. Default is \code{'RNA_network'}.}
+
+\item{store_network}{(bool) - Save the network directly (\code{TRUE},
+default) or return without saving on disk (\code{FALSE}).}
+
+\item{output_file}{(character) - Name of the output_file
+(if store_network == \code{TRUE}).}
+
+\item{threshold}{(interger, default 0) - Minimal threshold
+to select tf-gene edges.}
+
+\item{number_cores}{(interger, default 1) - Number of thread that should be
+used for the parallelizable methods.}
+
+\item{verbose}{(integer) - Display function messages. Set to 0 for no
+message displayed, >= 1 for more details.}
+}
+\value{
+(data.frame) - Return list of network interactions between genes
+}
+\description{
+This function will create a network from rna data (or in theory any data
+wtih genes as features).
+Different method should be implemented at some point (any suggestion is welcomed ! :) ),
+for now Genie3 is still the reference and only method available
+}
+\details{
+Method descriptions :
+\enumerate{
+\item Genie3
+Use tree random forest to infer regulatory networks :
+https://bioconductor.org/packages/release/bioc/html/GENIE3.html
+}
+}
+\examples{
+hummus <- compute_gene_network(
+                               hummus,
+                               gene_assay = "RNA",
+                               method = "GENIE3",
+                               verbose = 1,
+                               number_cores = 8,
+                               store_network = FALSE)
+
+}