--- a
+++ b/man/define_target_genes.Rd
@@ -0,0 +1,77 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/explore_network.R
+\name{define_target_genes}
+\alias{define_target_genes}
+\title{Define target genes from hummus object}
+\usage{
+define_target_genes(
+  hummus_object,
+  multiplex_names = NULL,
+  bipartites_names = NULL,
+  config_name = "target_genes_config.yml",
+  config_folder = "config",
+  tf_multiplex = "TF",
+  atac_multiplex = "peaks",
+  rna_multiplex = "RNA",
+  multilayer_f = "multilayer",
+  gene_list = NULL,
+  tf_list = NULL,
+  save = FALSE,
+  output_f = NULL,
+  return_df = TRUE,
+  suffix_bipartites = ".tsv",
+  njobs = 1
+)
+}
+\arguments{
+\item{hummus_object}{A hummus object}
+
+\item{multiplex_names}{A vector of multiplex names considered.
+It must be a subset of the names of the multiplexes in the hummus object.}
+
+\item{bipartites_names}{A vector of bipartites names considered.
+It must be a subset of the names of the bipartites in the hummus object.}
+
+\item{config_name}{The name of the config file to be created by hummuspy}
+
+\item{config_folder}{The folder where the config file will be created}
+
+\item{tf_multiplex}{The name of the multiplex containing the TFs}
+
+\item{atac_multiplex}{The name of the multiplex containing the ATAC-seq peaks}
+
+\item{rna_multiplex}{The name of the multiplex containing the RNA-seq genes}
+
+\item{multilayer_f}{The folder where the multilayer is stored}
+
+\item{gene_list}{A vector of genes to be considered for the target_genes
+(filtering is done on the genes before inferring the target_genes)}
+
+\item{tf_list}{A vector of TFs to be considered for the final target_genes
+(filtering is done on the TFs after inferring the target_genes)}
+
+\item{save}{A boolean indicating if the target_genes should be saved}
+
+\item{output_f}{The name of the file where the target_genes should be saved
+(if save == TRUE)}
+
+\item{return_df}{A boolean indicating if the target_genes should be returned
+as a dataframe}
+
+\item{suffix_bipartites}{A suffix to add to the bipartites names (to indicate
+the exact file location)}
+
+\item{njobs}{The number of jobs to be used to compute of the target_genes}
+}
+\value{
+A dataframe containing the target_genes (if return_df == TRUE)
+}
+\description{
+Calling the define_output function with output_type = 'target_genes'
+}
+\examples{
+target_genes <- define_target_genes(hummus_object = hummus,
+                            multilayer_f = multilayer_folder,
+                            njobs = 5)
+
+}