--- a
+++ b/man/bipartite_peaks2genes.Rd
@@ -0,0 +1,87 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bipartites.R
+\name{bipartite_peaks2genes}
+\alias{bipartite_peaks2genes}
+\title{Compute links between DNA regions and genenames}
+\usage{
+bipartite_peaks2genes(
+  hummus_object,
+  gene_assay = "RNA",
+  peak_assay = "peaks",
+  gene_multiplex_name = NULL,
+  peak_multiplex_name = NULL,
+  peak_to_gene_method = "Signac",
+  upstream = 500,
+  downstream = 500,
+  only_tss = TRUE,
+  store_network = FALSE,
+  output_file = NULL,
+  bipartite_name = "atac_rna"
+)
+}
+\arguments{
+\item{hummus_object}{(hummus_object) - Hummus object.}
+
+\item{gene_assay}{(character) - Name of assay containing the gene expression
+data. Default: "RNA".}
+
+\item{peak_assay}{(character) - Name of the assay containing the DNA regions
+(ATAC peaks). Default: "peaks".}
+
+\item{gene_multiplex_name}{(character) - Name of the multiplex containing the
+genes.
+If NULL, the name of the gene assay is used.}
+
+\item{peak_multiplex_name}{(character) - Name of the multiplex containing the
+DNA regions (ATAC peaks). If NULL, the name of the peak assay is used.}
+
+\item{peak_to_gene_method}{(character) - Method to use to compute the links
+between peaks and genes. Default: "Signac".
+\itemize{
+\item \code{'Signac'} - Use Signac::Extend to extend genes.
+\item \code{'GREAT'} - Not implemented yet.
+}}
+
+\item{upstream}{(int) - Upstream distance from TSS
+to consider as potential promoter.}
+
+\item{downstream}{(int) - Downstream distance from TSS
+to consider as potential promoter.}
+
+\item{only_tss}{(logical) - If TRUE, only TSS will be considered.}
+
+\item{store_network}{(bool) - Save the bipartite directly
+(\code{TRUE}, default) or return without saving on disk (\code{FALSE}).}
+
+\item{output_file}{(character) - Name of the output_file
+(if store_bipartite == \code{TRUE}). Default: NULL.}
+
+\item{bipartite_name}{(character) - Name of bipartite. Default: "atac_rna".}
+
+\item{verbose}{(integer) Display function messages.
+Set to 0 for no message displayed, >= 1 for more details. Default: 1.}
+}
+\value{
+hummus_object (hummus_object) - Hummus object w/ atac-rna bipartite
+added to the multilayer slot
+}
+\description{
+Compute and add bipartite between DNA regions and genenames to hummus object.
+Links are computed based on the distance between peaks and gene's TSS
+location from gene.range annotations.
+Call find_peaks_near_genes function, that can use different methods.
+}
+\examples{
+hummus <- bipartite_peaks2genes(
+                       hummus_object = hummus,
+                       gene_assay = "RNA",
+                       peak_assay = "peaks",
+                       gene_multiplex_name = "RNA",
+                       peak_multiplex_name = "peaks",
+                       peak_to_gene_method = "Signac",
+                       upstream = 500,
+                       downstream = 500,
+                       only_tss = TRUE,
+                       store_network = FALSE,
+                       bipartite_name = "atac_rna")
+}