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

In metaboGSE: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

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

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)

metaboGSE documentation built on Oct. 23, 2020, 8:14 p.m.