parse.metacyc.reaction: Parse MetaCyc reaction data (reactions.dat in attribute-value...

Description Usage Arguments Value Author(s) Examples

View source: R/parse.metacyc.reaction.R

Description

Parse MetaCyc reactions.dat file in attribute-value format. The output includes reaction ID, enzyme, EC number, pathway and equation

Usage

1

Arguments

datPath

Path to reactions.dat from MetaCyc (BioCyc or EcoCyc data also applicable)

Value

data.frame() object where data fields include

UNIQUE.ID
TYPES
ATOM.MAPPINGS
CITATIONS
COMMENT
CREDITS
DBLINKS
IN.PATHWAY
LEFT
PHYSIOLOGICALLY.RELEVANT.
REACTION.DIRECTION
RIGHT
CANNOT.BALANCE.
ENZYMATIC.REACTION
ORPHAN.
SPONTANEOUS.
RXN.LOCATIONS
EC.NUMBER
COMMON.NAME
TEMPLATE.FILE
SYNONYMS
SYSTEMATIC.NAME
DELTAG0
COMMENT.INTERNAL
ENZYMES.NOT.USED
REACTION.LIST
MEMBER.SORT.FN
STD.REDUCTION.POTENTIAL
PREDECESSORS
PRIMARIES
SIGNAL
equation
LIGAND.RXN
PLANTCYC
METACYC
RHEA
UNIPROT
PIR
LIGAND
BRENDA
superNode

Author(s)

Byoungnam Min <[email protected]>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

Examples

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url = "http://bioinformatics.ai.sri.com/ptools/flatfile-samples/reactions.dat"
tmpdest = tempfile(pattern = "reactions")
download.file(url, destfile=tmpdest)

direction = "LEFT-TO-RIGHT" # sample data is old, so don't mind this code.
sample.reactions = parse.metacyc.reaction(datPath=tmpdest)
print(sample.reactions)

RbioRXN documentation built on May 29, 2017, 10:56 a.m.