scoreGraph: Score metabolic graph

View source: R/gatom.R

scoreGraphR Documentation

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 May 3, 2024, 3:44 p.m.