Cicero wrapper function for the compute_atac_peak_network function

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.

Usage

run_cicero_wrapper(
  hummus,
  atac_assay,
  genome,
  window,
  number_cells_per_clusters,
  sample_num,
  seed,
  verbose,
  threshold,
  reduction_method = "UMAP"
)

Arguments

hummus: A hummus object
atac_assay: The name of the assay containing the scATAC-seq data
genome: The genome object
window: The window size used by Cicero to compute the coaccess score
number_cells_per_clusters: The number of cells per cluster used by Cicero to compute the coaccess score
sample_num: The number of samples used by Cicero to compute the coaccess score
seed: The seed used by Cicero to compute the coaccess score
verbose: The verbosity level
threshold: The threshold used to filter edges based on the coaccess score
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