Function to bootstrap Epoch reconstruction

Source: R/network_comparison.R

Function to bootstrap Epoch reconstruction

sample_and_epoch_reconstruct(
  matrix,
  meta_data,
  tfs,
  n_reconstructions = 10,
  ncells_per_sample = 400,
  p_value = 0.05,
  zThresh = 5,
  pseudotime_column = "pseudotime",
  group_column = "leiden",
  method = "pearson",
  crossweight = FALSE,
  limit_to = NULL
)

Arguments

matrix

genes-by-cells expression matrix

meta_data

sample table

tfs

TFs

n_reconstructions

the number of networks to reconstruct

ncells_per_sample

the number of cells to sample for each reconstruction

p_value

p-value threshold for selecting dynamic genes

zThresh

z-score threshold in static reconstruction

pseudotime_column

column name in meta_data with pseudotime annotation

group_column

column name in meta_data for restricting reconstruction

method

CLR method, either "pearson" or "MI"

crossweight

whether or not to perform crossweighting

limit_to

vector of genes. If not NULL, will skip finding dynamic genes and use genes in limit_to for reconstruction

Value

list of grnDFs