sample_and_epoch_reconstruct: Function to bootstrap Epoch reconstruction

In pcahan1/epoch: Dynamic GRN reconstruction from single cell RNA-Seq data

Description

Function to bootstrap Epoch reconstruction

Usage

sample_and_epoch_reconstruct(
  expX,
  sampTab,
  tfs,
  n_reconstructions = 10,
  ncells_per_sample = 400,
  pThresh = 0.05,
  zThresh = 5,
  pseudotime_column = "dpt_pseudotime",
  group_column = "leiden",
  method = "pearson",
  crossweight = FALSE,
  limit_to = NULL
)

Arguments

expX	genes-by-cells expression matrix
sampTab	sample table
tfs	TFs
n_reconstructions	the number of networks to reconstruct
ncells_per_sample	the number of cells to sample for each reconstruction
pThresh	p-value threshold for selecting dynamic genes
zThresh	z-score threshold in static reconstruction
pseudotime_column	column name in sampTab with pseudotime annotation
group_column	column name in sampTab 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

pcahan1/epoch documentation built on Feb. 14, 2022, 1:57 a.m.