Description Usage Value Note Author(s) References See Also Examples
View source: R/get.metacyc.all.R
This function first retrieves all MetaCyc reaction IDs and download BioPAX level 3 for each reaction, then parse to generate data.frame() object. Note that because this function interacts with BioCyc web service for every reaction, it will take many hours depending on your network speed. Thus, we strongly recommend to use parse.metacyc.reaction() and parse.metacyc.compound() functions in this package after manually downloading MetaCyc from http://biocyc.org/download.shtml
NOTE: The MetaCyc server is occasionally unavailable, so this function accesses our own server as additional resource after trying original server. Our server may not contain latest data.
1 |
R data.frame() object where data fields indclude
MetaCyc |
MetaCyc ID |
name |
Reaction equation with chemical standard name |
ec_number |
E.C number |
name_id |
Reaction equation with MetaCyc compound ID |
We strongly recommend using parse.metacyc.reaction() and parse.metacyc.reaction() functions because of long running process. These two functions need "dat" files downloaded from MetaCyc. See http://biocyc.org/download.shtml
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
MetaCyc download page: http://biocyc.org/download.shtml
MetaCyc web services: http://biocyc.org/web-services.shtml
parse.metacyc.reaction
parse.metacyc.compound
1 2 3 4 | # Not run:
## metacycAll = get.metacyc.all()
## head(metacycAll)
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