GO-class {AnnBuilder}R Documentation

Class "GO" a class to handle data from Gene Ontology

Description

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 from the Class

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

Slots

srcUrl:
Object of class "character", from class "pubRepo" a character string for the url of the source data from Gene Ontology
parser:
Object of class "character", from class "pubRepo" not in use
baseFile:
Object of class "character", from class "pubRepo" not in use

Extends

Class "pubRepo", directly.

Methods

readData
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

Note

This class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.godatabase.org

See Also

pubRepo-class

Examples

# Read a truncated version of GO.xml from Bioconductor
go <- GO(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml", built = "NA")
goxml <- readData(go, xml = TRUE)

[Package AnnBuilder version 1.4.21 Index]