GEO-class {AnnBuilder}R Documentation

Class "GEO" represents a GEO object that reads/downloads data from the GEO web site

Description

The GEO web site contains data files represented by GEO accession numbers. Class GEO reads/downloads data files from the site if correct url and GEO accession numbers are provided

Objects from the Class

Objects can be created by calls of the form new("UG", ...). A constructor (GEO) is available and should be used to instantiate objects of this class

Slots

srcUrl:
Object of class "character", from class "pubRepo" - a character string for the url of a CGI script that handles data requests, which is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? at the time of writing

Extends

Class "pubRepo", directly.

Methods

readData
signature(object = "GEO"): reads data from GEO and then parses the data to a matrix

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

Programming with data

See Also

queryGEO,pubRepo-class

Examples

    if(interactive()){
        geo <- GEO("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
        # The GEOAccNum may be invalid due to changes at GEO site
        data <- readData(geo, GEOAccNum = "GPL16" )
    }

[Package AnnBuilder version 1.4.21 Index]