Simulate the effect of gene perturbation on the gene regulatory network.
This function propagates the perturbation signal through the GRN to predict
changes in gene expression.
Usage
simulate_shift(
oracle,
perturb_condition,
n_propagation = 3,
GRN_unit = NULL,
clip_delta_X = FALSE,
ignore_warning = FALSE
)
Arguments
- oracle
Oracle object with fitted GRN
- perturb_condition
Named list: gene -> expression value
- n_propagation
Number of signal propagation steps (1-5)
- GRN_unit
Which GRN to use: "cluster" or "whole"
- clip_delta_X
Clip simulated values to original range
- ignore_warning
Ignore validation warnings
Value
Modified Oracle object with simulation results