metaboGSE (version 1.2.5)

submnet: Simulation of gene removal-based submodel series with a given ranking

Description

This function simulates the construction of a series of submodels by removing genes in a given ranking.

Usage

submnet(
  model,
  fn,
  rank.best = "expr",
  gene.sets = NULL,
  mc.cores = 1,
  obj.react = NA,
  timeout = 12,
  tol = SYBIL_SETTINGS("TOLERANCE"),
  solver = SYBIL_SETTINGS("SOLVER"),
  method = SYBIL_SETTINGS("METHOD")
)

Arguments

model

An object of class modelorg indicating the weighted rescue model obtained from the rescue process.

fn

An object returned by the fitness function.

rank.best

Name of a ranking among simulated ones. Default: "expr".

gene.sets

Named list of gene sets for gene set enrichment analysis. Default: NULL, depletion fraction of gene sets should be further computed for gene set enrichment analysis.

mc.cores

The number of cores to use (at least 1), i.e. at most how many child processes will be run simultaneously. Default: 1.

obj.react

A string indicating objective reaction ID. Default: reaction producing BIOMASS.

timeout

The maximum time in seconds to allow for LP call to return. Default: 12.

tol

The maximum value to be considered null. Default: SYBIL_SETTINGS("TOLERANCE").

solver

sybil solver. Default: SYBIL_SETTINGS("SOLVER").

method

sybil method. Default: SYBIL_SETTINGS("METHOD").

Value

An object of class scoreGeneDel for the submodel construction simulation.

Examples

# NOT RUN {
data(Ec_core)
mod <- rescue(Ec_core, target=0.1)
mod.weight <- changeObjFunc(mod$rescue, react=rownames(mod$coef), obj_coef=mod$coef)
ranks <- list(
   rep.1=data.frame(
       expr=setNames(rnorm(length(sybil::allGenes(mod.weight)), mean=5, sd=4),
           sybil::allGenes(mod.weight))),
   rep.2=data.frame(
       expr=setNames(rnorm(length(sybil::allGenes(mod.weight)), mean=5, sd=4.1),
           sybil::allGenes(mod.weight))))
fn <- fitness(model=mod.weight, ranks=ranks, step=200, draw.num=1)
gene.sets <- list(X1=head(sybil::allGenes(mod.weight)), X2=tail(sybil::allGenes(mod.weight)))
sgd <- submnet(model=mod.weight, fn=fn, rank.best="expr",
               obj.react="Biomass_Ecoli_core_w_GAM", gene.sets=gene.sets)
# }