metaboGSE (version 1.2.5)

scoreGeneDel: Structure of Class "scoreGeneDel"

Description

Structure of the class scoreGeneDel. Objects of this class are returned by the function submnet.

Usage

scoreGeneDel(
  model = NULL,
  condition = NA,
  fitness.random = NULL,
  fitness.ranks = NULL,
  fitness.id.random = NULL,
  fitness.id.ranks = NULL,
  ess.gene = NULL,
  ess.reaction = NULL,
  gene.del = NULL,
  gene.sets = NULL,
  ratio.GS = NULL,
  sub.genes = NULL,
  sub.reacs = NULL,
  sub.metas = NULL,
  rescue.met = NULL
)

Arguments

model

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

condition

The experimental condition ID.

fitness.random

Random-based fitness with weighting scheme.

fitness.ranks

Ranks-based fitness with weighting scheme.

fitness.id.random

Random-based fitness without weighting scheme.

fitness.id.ranks

Ranks-based fitness without weighting scheme.

ess.gene

Percentages of essential genes. The computation of essentiality is deprecated in this version.

ess.reaction

Percentages of essential reactions. The computation of essentiality is deprecated in this version.

gene.del

Number of deleted genes.

gene.sets

Gene sets.

ratio.GS

Percentages of remaining genes in each gene set.

sub.genes

Remaining genes in submodels after propagation.

sub.reacs

Remaining reactions in submodels after propagation.

sub.metas

Remaining metabolites in submodels after propagation.

rescue.met

Fraction of every rescued metabolite among random draws.

Value

An object of class scoreGeneDel.

Examples

# NOT RUN {
data(yarliSubmnets)
attributes(yarliSubmnets[[1]])
# }