scoreGraph: Score metabolic graph

In ctlab/gatom: Finding an Active Metabolic Module in Atom Transition Network

Score metabolic graph

Description

Score metabolic graph

Usage

scoreGraph(
  g,
  k.gene,
  k.met,
  vertex.threshold.min = 0.1,
  edge.threshold.min = 0.1,
  met.score.coef = 1,
  show.warnings = TRUE,
  raw = FALSE
)

Arguments

g	Metabolic graph obtained with makeMetabolic graph function
k.gene	Number of gene signals to be scored positively, the higher is the number, the larger will be the resulting module. If set to NULL, genes will not be used for scoring.
k.met	Number of metabolite signals to be scored positively, the higher is the number, the larger will be the resulting module. If set to NULL, metabolites will not be used for scoring.
vertex.threshold.min	The worst acceptable estimated FDR for vertices. If necessary number of positive metabolite signals will be decreased from 'k.met' to reach this threshold. Default value is 0.1.
edge.threshold.min	The worst acceptable estimated FDR for vertices. If necessary number of positive metabolite signals will be decreased from 'k.gene' to reach this threshold. Default value is 0.1.
met.score.coef	Coefficient on which all vertex weights are multiplied. Can be used to balance vertex and edge weights. Default values is 1.
show.warnings	whether to show warnings
raw	whether to return raw scored graph, not a SGMWCS instance. Default to FALSE.

Value

SGMWCS instance or scored igraph object

Examples

data("gEx")
gs <- scoreGraph(g = gEx, k.gene = 25, k.met = 25)

ctlab/gatom documentation built on Oct. 22, 2023, 4:30 p.m.