% 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")

}