Find TF modules in regulatory network

Find TF modules in regulatory network

find_modules(object, ...)

# S4 method for class 'Network'
find_modules(
  object,
  p_thresh = 0.05,
  rsq_thresh = 0.1,
  nvar_thresh = 10,
  min_genes_per_module = 5,
  xgb_method = c("tf", "target"),
  xgb_top = 50,
  verbose = TRUE,
  ...
)

# S4 method for class 'CSNObject'
find_modules(
  object,
  network = DefaultNetwork(object),
  p_thresh = 0.05,
  rsq_thresh = 0.1,
  nvar_thresh = 10,
  min_genes_per_module = 5,
  ...
)

Arguments

object

An object.

...

Arguments for other methods

p_thresh

Float indicating the significance threshold on the adjusted p-value.

rsq_thresh

Float indicating the \(R^2\) threshold on the adjusted p-value.

nvar_thresh

Integer indicating the minimum number of variables in the model.

min_genes_per_module

Integer indicating the minimum number of genes in a module.

xgb_method

Method to get modules from xgb models tf - Choose top targets for each TF. target - Choose top TFs for each target gene.

xgb_top

Interger indicating how many top targets/TFs to return.

verbose

Print messages.

network

Name of the network to use.

Value

A Network object.

A CSNObject object