GO-class {AnnBuilder} | R Documentation |
This class is a sub-class of pubRepo that is implemented
specifically to parse data from Gene Ontology. readData
has been over written to process Gene Ontology data
Objects can be created by calls of the form new("GO", ...)
.
A constructor (GO
is available and should be used to
instantiate objects of GO).
srcUrl
:"character", from class
"pubRepo"
a character string for the url of the source data
from Gene Ontologyparser
:"character", from class
"pubRepo"
not in usebaseFile
:"character", from
class "pubRepo"
not in use
Class "pubRepo"
, directly.
signature(object = "GO")
: Downloads/processes
go_xxx-termdb from Gene Ontology, where xxx is a date. If argument
xml is set to be TRUE, the data file will be parsed and a matrix
with three columns will be returned. The first column is for GO
ids, second for the GO ids of its direct parents, and third for
the ontology term defined by Gene Ontology. Otherwise, the data
(not in xml form) will be read in using readLines
Jianhua Zhang