% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/method_wrappers.R
\name{run_cicero_wrapper}
\alias{run_cicero_wrapper}
\title{Cicero wrapper function for the compute_atac_peak_network function}
\usage{
run_cicero_wrapper(
  hummus,
  atac_assay,
  genome,
  window,
  number_cells_per_clusters,
  sample_num,
  seed,
  verbose,
  threshold,
  reduction_method = "UMAP"
)
}
\arguments{
\item{hummus}{A hummus object}

\item{atac_assay}{The name of the assay containing the scATAC-seq data}

\item{genome}{The genome object}

\item{window}{The window size used by Cicero to compute the coaccess score}

\item{number_cells_per_clusters}{The number of cells per cluster used by
Cicero to compute the coaccess score}

\item{sample_num}{The number of samples used by Cicero to compute the
coaccess score}

\item{seed}{The seed used by Cicero to compute the coaccess score}

\item{verbose}{The verbosity level}

\item{threshold}{The threshold used to filter edges based on the coaccess
score}

\item{reduction_method}{The method used by monocle3 to reduce the dimension
of the scATAC-seq data before defining the pseudocells. The default is UMAP.}
}
\value{
A data frame containing the peak network
}
\description{
This function is a wrapper for the compute_atac_peak_network
function in layers.R. It computes the peak network from scATAC-seq data
using Cicero. It returns a data frame with the peak network. The data frame
also contains the coaccess score for each edge. The coaccess score is the
probability that two peaks are accessible in the same cell. The coaccess
score is computed by Cicero. Edges are filtered based on the coaccess score.
Only edges with a coaccess score > threshold are kept.
}