GGN: Construct Gene-Gene Network

In scPOEM: Single-Cell Meta-Path Based Omic Embedding

Construct Gene-Gene Network

Description

Construct the gene-gene network via principle component regression.

Usage

GGN(
  Y,
  dirpath = tempdir(),
  count_device = 1,
  nComp = 5,
  rebuild_GGN = TRUE,
  save_file = TRUE,
  python_env = "scPOEM_env"
)

Arguments

Y	The scRNA-seq data, sparse matrix.
dirpath	The folder path to read or write file.
count_device	The number of cpus used to train the Lasso model.
nComp	The number of PCs used for regression
rebuild_GGN	Logical. Whether to rebuild the gene-gene network (GGN) from scratch. If FALSE, the function will attempt to read from GGN.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.
python_env	Name or path of the Python environment to be used.

Value

The GGN network.

Examples

library(scPOEM)
dirpath <- "./example_data"
# Download single mode example data
data(example_data_single)
# Construct GGN net.
gg_net <- GGN(example_data_single$Y,
              file.path(dirpath, "single"),
              save_file=FALSE)

scPOEM documentation built on Aug. 28, 2025, 9:09 a.m.