% 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)

}