makeOrgGatomAnnotation: Create an organism annotation object for network analysis

View source: R/annotation.R

makeOrgGatomAnnotationR Documentation

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.