--- a
+++ b/man/bipartite_tfs2peaks.Rd
@@ -0,0 +1,70 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/bipartites.R
+\name{bipartite_tfs2peaks}
+\alias{bipartite_tfs2peaks}
+\title{Compute links between TFs and DNA regions (ATAC peaks)}
+\usage{
+bipartite_tfs2peaks(
+  hummus_object,
+  tf_expr_assay = "RNA",
+  peak_assay = "peaks",
+  tf_multiplex_name = NULL,
+  peak_multiplex_name = NULL,
+  genome,
+  store_network = FALSE,
+  output_file = NULL,
+  verbose = 1,
+  bipartite_name = "tf_peak"
+)
+}
+\arguments{
+\item{hummus_object}{(hummus_object) - Hummus object.}
+
+\item{tf_expr_assay}{(character) - Name of assay containing the TF expression
+data. If NULL, all TFs with a motif are used. Default: "RNA".}
+
+\item{peak_assay}{(character) - Name of the assay containing the DNA regions
+(ATAC peaks). Default: "peaks".}
+
+\item{tf_multiplex_name}{(character) - Name of multiplex containing the TFs.
+If NULL, the name of the TF 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{genome}{(BSgenome object) - Reference genome.}
+
+\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{verbose}{(integer) Display function messages.
+Set to 0 for no message displayed, >= 1 for more details. Default: 1.}
+
+\item{bipartite_name}{(character) - Name of bipartite. Default: "tf_peak".}
+}
+\value{
+hummus_object (hummus_object) - Hummus object with TF-peak bipartite
+added to the multilayer slot
+}
+\description{
+Compute and add bipartite between TFs and DNA regions to hummus object.
+Links are computed based on the binding motifs of TFs and their locations
+on a reference genome.
+Currently based on Signac AddMotifs function (--> motifmachR, itself based on
+MOODs algorithm).
+}
+\examples{
+hummus <- bipartite_tfs2peaks(
+                     hummus_object = hummus,
+                     tf_expr_assay = "RNA",
+                     peak_assay = "peaks",
+                     tf_multiplex_name = "TF",
+                     peak_multiplex_name = "peaks",
+          genome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
+                     store_network = FALSE,
+                     verbose = 1,
+                     bipartite_name = "tf_peak")
+}