scPOEM (version 0.1.3)

PPN: Construct Peak-Peak Network

Description

Construct peak-peak network.

Usage

PPN(
  X,
  peak_data,
  cell_data,
  genome,
  dirpath = tempdir(),
  rebuild_PPN = TRUE,
  save_file = TRUE,
  seed = NULL
)

Value

The PPN network.

Arguments

X

The scATAC-seq data, sparse matrix.

peak_data

The information for peaks, must have a col names "peak_name".

cell_data

The information for cells, must have a col names "cell_name".

genome

The genome length for the species.

dirpath

The folder path to read or write file.

rebuild_PPN

Logical. Whether to rebuild the peak-peak network (PPN) from scratch. If FALSE, the function will attempt to read from PPN.mtx under dirpath/test in single mode or dirpath/state_name/test in compare mode.

save_file

Logical, whether to save the output to a file.

seed

An integer specifying the random seed to ensure reproducible results.

Examples

# \donttest{
library(scPOEM)
library(monocle)
dirpath <- "./example_data"
# Download single mode example data
data(example_data_single)
# Construct PPN net.
pp_net <- PPN(example_data_single$X,
              example_data_single$peak_data,
              example_data_single$cell_data,
              example_data_single$genome,
              file.path(dirpath, "single"),
              save_file=FALSE)
# }