Compute pseudotime based on transition probability

Estimates pseudotime ordering based on the perturbation-induced transition probability structure.

Usage

compute_pseudotime(
  oracle,
  start_cells,
  method = c("markov", "diffusion"),
  n_steps = 500,
  n_duplicates = 100
)

Arguments

oracle

Oracle object with transition probabilities

start_cells

Starting cell indices (1-indexed)

method

Method: "markov" (simulation-based) or "diffusion"

n_steps

Number of steps for Markov simulation

n_duplicates

Duplicates per cell for Markov simulation

Value

Named vector of pseudotime values