scPOEM (version 0.1.3)

GGN: 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"
)

Value

The GGN network.

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.

Examples

# \donttest{
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)
# }