Samplelineage: Sample Cell Identity Factors via Brownian motion, based on...

In Galaxeee/TedSim: Temporal Dynamics Simulation of scRNA-seq and CRISR/Cas9 lineage barcodes

Sample Cell Identity Factors via Brownian motion, based on the cell lineage

Description

Sample Cell Identity Factors via Brownian motion, based on the cell lineage

Usage

Samplelineage(
  par,
  depth,
  anc_state,
  edges,
  muts = NULL,
  p_d = 0.1,
  mu = 0.1,
  edges_state,
  sif_mean = NULL,
  S = NULL,
  p_a = 0.8,
  cif = NULL,
  flag = NULL,
  barcode = NULL,
  N_ms = NULL,
  unif_on = FALSE,
  lambda = NULL
)

Arguments

par	current parent node label
depth	current depth of the parent node
anc_state	Cell Identity Factor value of the parent node
edges	edge list of the cell lineage tree
muts	the mutation barcode matrix
p_d	whether or not to have dropouts
mu	mutation rate
edges_state	edge list of the state tree
sif_mean	state identity factor values
S	state and state identity factor of the parent
p_a	asymmetric division rate
cif	cell identity factor matrix
flag	whether or not generate barcode along with gene expressions
barcode	current barcode of the parent node
N_ms	Number of possible mutated states
unif_on	if unif_on is TRUE, the mutated states will be synthetically generated using uniform distribution; otherwise, it will be sampled from a real dataset
lambda	a num vector that indicates the value of lambda that weights the additional random walk value for different depths

Galaxeee/TedSim documentation built on Oct. 2, 2022, 1:25 a.m.