run the in silico perturbation experiment on the fitted S-system network model

perturb {ssGrid}

R Documentation

run the in silico perturbation experiment on the fitted S-system network model

Description

Usage

perturb(network, geneIds,
    type = "knockdown",
    magnitude = 0.8,
    kicks = 1,
    start = 0.1,
    final.time = 0,
    context = NULL,
    export = NULL);

Arguments

network

the fitted network model, which is the output of the sfit api. [as SSystemNetwork]

geneIds

a character vector of the target gene id of the perturbation.

type

the perturbation type: knockdown(default), knockout or overexpress. [as string]

magnitude

the perturbation strength: for the knockdown, 0.8 means that the target gene loses 80% of its activity; for the overexpress, 1 means that an extra 100% of the baseline expression will be added to the target gene. [as double]

kicks

the times that the perturbation will be applied, a periodic stimulation is used to simulate a sustained treatment. [as integer]

start

the time point that the first perturbation kick is applied. [as double]

final.time

the final time of the simulation, zero means the end of the fitted time axis. [as double]

context

the optional sample context(the ODE initial state), which should be created via the sgrid_context api. [as list]

export

the optional output directory for save the trajectory files of each perturbation design; nothing will be written if this parameter is not provided. [as string]

env

[as Environment]

Authors

biosystem

Value

a ScreeningResult object which could be converted to a data.frame via as.data.frame, or a R# error message object.

clr value class

ScreeningResult

Examples

 let ctx = sgrid_context(network, "/data/pseudobulk_context_A.csv");
 let resp = perturb(network, c("ABCD1","ACLY"), context = ctx, export = "/tmp/ko");

[Package ssGrid version 1.0.0.0 Index]