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Construct network for single target gene

Source: R/single_network.R
single_network.Rd

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

Whether to use cross-validation. Default is FALSE.

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

Whether to print progress messages. Default is TRUE.

...

Parameters for other methods.

Value

A data frame of the single target gene network. The data frame has three columns: regulator, target, and weight.

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"
)
#> ! [2025-10-16 02:37:04] Less than 2 regulators found while modeling: g1
#> NULL