% 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")
}