helpers_general: general helper function

In zgzhao/gmetab: syzMetab: R package for metabolic network analysis

Description

general helpers for retrieving data from KDataSet, reactions list or mgraph object

Details

All functions below are generic functions. Function names are self-explanatory:

• pathInfo(object): pathway info

• Organism(object): organism name

• Species(object): alias of Organism

• Genes(object): all genes/orthologs

• Compounds(object): all compounds

• Chemicals(object): alias of Compounds

• Reactions(object, list.only=TRUE): reactions list or ReactionSet object (list.only=FALSE for mgraph object)

Author(s)

ZG Zhao

Examples

library(syzMetab)
d.path <- file.path(path.package("syzMetab"), "KEGG")
pp <- make_kdset("ko00010", d.path)
##
## KEGG pathway data
pathInfo(pp)
Organism(pp)
Compounds(pp)
Chemicals(pp)
Genes(pp)
Reactions(pp)
##
## metabolic graph
gg <- make_mgraph(pp)
Organism(gg)
Compounds(gg)
Chemicals(gg)
Genes(gg)
Reactions(gg)
Reactions(gg, list.only=FALSE)

zgzhao/gmetab documentation built on Dec. 23, 2021, 9:17 p.m.