makeOrgGatomAnnotation: Create an organism annotation object for network analysis

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

Create an organism annotation object for network analysis

Description

Create an organism annotation object for network analysis

Usage

makeOrgGatomAnnotation(
  org.db,
  idColumns = c(Entrez = "ENTREZID", RefSeq = "REFSEQ", Ensembl = "ENSEMBL", Symbol =
    "SYMBOL"),
  nameColumn = "SYMBOL",
  enzymeColumn = "ENZYME",
  appendEnzymesFromKegg = TRUE,
  appendOrthologiesFromKegg = TRUE,
  filterNonSpecificEnzymes = TRUE,
  keggOrgCode = NULL
)

Arguments

org.db	Bioconductor org.db object, e.g. org.Mm.eg.db
idColumns	vector of column names from 'org.db' object to creat ID mappings. First ID will be used as a base identifier, should be compatible with KEGG and Reactome databases.
nameColumn	column with a human readable gene symbol. Default to "SYMBOL".
enzymeColumn	column with an Enzyme Commission ID. Default to "ENZYME".
appendEnzymesFromKegg	if TRUE, KEGG databases will be sued to extend gene to enzyme mappings obtained from org.db package.
appendOrthologiesFromKegg	if TRUE, KEGG database will be sued to extend gene to orthology mappings obtained from org.db package
filterNonSpecificEnzymes	if TRUE, will filter out non-specific enzymes from gene to enzyme mappings obtained from org.db package
keggOrgCode	KEGG organism code, e.g. "mmu". If set to NULL, the code is determined automatically.

Value

organism annotation object that will be used for network analysis

Examples

library(org.Mm.eg.db)
org.Mm.eg.gatom.anno <- makeOrgGatomAnnotation(org.db = org.Mm.eg.db)

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