% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/layers.R
\name{compute_atac_peak_network}
\alias{compute_atac_peak_network}
\title{Compute peak network from scATAC-seq data}
\usage{
compute_atac_peak_network(
  hummus,
  atac_assay = "peaks",
  genome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
  method = "cicero",
  multiplex_name = NULL,
  network_name = NULL,
  store_network = FALSE,
  output_file = NULL,
  threshold = 0,
  number_cells_per_clusters = 50,
  sample_num = 100,
  seed = 2025,
  verbose = 1,
  window = 5e+05,
  reduction_method = "UMAP"
)
}
\arguments{
\item{hummus}{(Hummus_Object) - Hummus object}

\item{atac_assay}{(character) - Name of the assay containing the atac
peaks data.}

\item{genome}{(BSgenome) - Genome used to compute the distance between peaks.}

\item{method}{(character) - Method used to infer network edges.
\itemize{
\item \code{'cicero'} - Use cicero to infer regulatory networks.
\item \code{'Other method'} - TO DO.
}}

\item{multiplex_name}{(character) - Name of the multiplex to add the network
to. Default is \code{'peaks'}.}

\item{network_name}{(character) - Name of the network in the multiplex to
add the network to. Default is \code{'peak_network'}.}

\item{store_network}{(bool) - Save the network directly (\code{TRUE},
default) or return without saving on disk (\code{FALSE}).}

\item{output_file}{(character) - Name of the output_file
(if store_network == \code{TRUE}).}

\item{threshold}{(interger, default 0) - Minimal threshold to select tf-gene
edges.}

\item{number_cells_per_clusters}{(integer) - Number of cells grouped by
territory to define pseudocells}

\item{sample_num}{(integer | Cicero) - Number of pseudocells to sample from
each territory. Default is 100.}

\item{seed}{(integer | Cicero) - Seed used to sample pseudocells. Default is
2025}

\item{verbose}{(integer) - Display function messages. Set to 0 for no
message displayed, >= 1 for more details.}

\item{window}{(integer) - Size of window to consider potential
cis-regulatory cooperations between peaks. Default is 500K base pairs.}

\item{reduction_method}{(character | Cicero) - Method used to reduce dimensionality
of the data to identify territories. Default is \code{'UMAP'}.}
}
\value{
(data.frame) - Return list of network interactions between peaks
}
\description{
This function will create a network from atac data (or in theory any data
wtih peaks coordinates as features).
Different method should be implemented at some point (e.g. RENIN),
for now Cicero is still the reference and only method available
}
\details{
Method descriptions :
\enumerate{
\item Cicero
Use patial corelation between peaks that are in a given window (e.g. :
less distant than 500K base pairs)
}
}
\examples{
hummus <- compute_atac_peak_network(hummus)

}