makeMetabolicGraph: Creates metabolic graph based on specified data

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

Creates metabolic graph based on specified data

Description

Creates metabolic graph based on specified data

Usage

makeMetabolicGraph(
  network,
  topology = c("atoms", "metabolites"),
  org.gatom.anno,
  gene.de,
  gene.de.meta = getGeneDEMeta(gene.de, org.gatom.anno),
  gene.keep.top = 12000,
  met.db,
  met.de,
  met.de.meta = getMetDEMeta(met.de, met.db),
  met.to.filter = fread(system.file("extdata", "mets2mask.lst", package = "gatom"))$ID,
  gene2reaction.extra = NULL,
  keepReactionsWithoutEnzymes = FALSE,
  largest.component = TRUE
)

Arguments

network	Network object
topology	Way to determine network vertices
org.gatom.anno	Organism annotation object
gene.de	Table with the differential gene expression, set to NULL if absent
gene.de.meta	Annotation of 'gene.de' table
gene.keep.top	Only the 'gene.keep.top' of the most expressed genes will be kept for the network
met.db	Metabolite database
met.de	Table with the differential expression for metabolites, set to NULL if absent
met.de.meta	Annotation of 'met.de' table
met.to.filter	List of metabolites to filter from the network
gene2reaction.extra	Additional gene to reaction mappings. Should be a data.table with 'gene' and 'reaction' columns
keepReactionsWithoutEnzymes	If TRUE, keep reactions that have no annotated enzymes, thus expanding the network but including some reactions which are not possible in the considered species.
largest.component	If TRUE, only the largest connected component is returned

Value

igraph object created from input data

Examples

data("gene.de.rawEx")
data("met.de.rawEx")
data("met.kegg.dbEx")
data("networkEx")
data("org.Mm.eg.gatom.annoEx")
g <- makeMetabolicGraph(network = networkEx, topology = "atoms",
                   org.gatom.anno = org.Mm.eg.gatom.annoEx,
                   gene.de = gene.de.rawEx, met.db = met.kegg.dbEx,
                   met.de = met.de.rawEx)

ctlab/gatom documentation built on May 3, 2024, 3:44 p.m.