Construct network for single target gene

Usage

single_network(
  matrix,
  regulators,
  target,
  cross_validation = FALSE,
  seed = 1,
  penalty = "L0",
  r_squared_threshold = 0,
  n_folds = 5,
  verbose = TRUE,
  ...
)

Arguments

matrix: An expression matrix.
regulators: The regulator genes for which to infer the regulatory network.
target: The target gene.
cross_validation: Logical value, default is FALSE, whether to use cross-validation.
seed: The random seed for cross-validation, default is 1.
penalty: The type of regularization, default is L0. This can take either one of the following choices: L0, L0L1, and L0L2. For high-dimensional and sparse data, L0L2 is more effective.
r_squared_threshold: Threshold of \(R^2\) coefficient, default is 0.
n_folds: The number of folds for cross-validation, default is 5.
verbose: Logical value, default is TRUE, whether to print progress messages.
...: Parameters for other methods.

Value

A data frame of the single target gene network. The data frame has three columns:

regulator: The regulator genes.
target: The target gene.
weight: The weight of the regulator gene on the target gene.

Examples

data("example_matrix")
head(
  single_network(
    example_matrix,
    regulators = colnames(example_matrix),
    target = "g1"
  )
)
#>   regulator target       weight
#> 1       g10     g1  0.009932787
#> 2       g11     g1  0.010286958
#> 3       g12     g1  0.017584462
#> 4       g13     g1 -0.002483363
#> 5       g14     g1 -0.021346832
#> 6       g15     g1  0.027390264
head(
  single_network(
    example_matrix,
    regulators = colnames(example_matrix),
    target = "g1",
    cross_validation = TRUE
  )
)
#>   regulator target       weight
#> 1       g10     g1  0.009932787
#> 2       g11     g1  0.010286958
#> 3       g12     g1  0.017584462
#> 4       g13     g1 -0.002483363
#> 5       g14     g1 -0.021346832
#> 6       g15     g1  0.027390264

single_network(
  example_matrix,
  regulators = c("g1", "g2", "g3"),
  target = "g1"
)
#>   regulator target     weight
#> 1        g2     g1  0.9876086
#> 2        g3     g1 -0.1569370
single_network(
  example_matrix,
  regulators = c("g1", "g2"),
  target = "g1"
)
#> ! [2025-05-07 09:38:57] less than 2 regulators found while modeling: g1
#> NULL