find_modules: Find TF modules in regulatory network

In quadbiolab/Pando: Inferring regulomes from multi-modal single-cell genomics data

Find TF modules in regulatory network

Description

Find TF modules in regulatory network

Usage

find_modules(object, ...)

## S3 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
)

## S3 method for class 'GRNData'
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.
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 GRNData object.

quadbiolab/Pando documentation built on April 22, 2024, 8:14 a.m.