Class "pubRepo" a generic class for downloading/parsing data provided by various public data repositories

Description

This class provides the basic functions to download/parser data from different public data repositories. More specific functions can be provided by extending this class to include source specific features

Objects from the Class

Objects can be created by calls of the form new("pubRepo", ...). A constructor (pubRepo is provided and should be used to create objects of this class.

Slots

srcUrl:

Object of class "character" a character string for the url of a data source from a public repository

parser:

Object of class "character" a character string for the name of a file that will be used as part of perl script to parse the source data. Parser is a segment of perl code containing instructions on how the source data will be processed and the content and format of the output

baseFile:

Object of class "character" a character string for the name of a file that will be used as the base to process the source data. Data from the source that are related to elements in the base file will be extracted. baseFile is assumed to be a two folumn file with the first column being some type of arbitrary ids (e.g. Affymetrix probe ids) and the second cloumn being the corresponding ids of a given public repository (e.g. GenBank accession numbers or UniGene ids)

Methods

baseFile<-

signature(object = "pubRepo"): Sets the value for baseFile

baseFile

signature(object = "pubRepo"): Gets the value for baseFile

downloadData

signature(object = "pubRepo"): Downloads data from a data source defined by srcUrl

parseData

signature(object = "pubRepo"): DownLoads/parses data from a data source defined by srcUrl

parser<-

signature(object = "pubRepo"): Sets the value for parser

parser

signature(object = "pubRepo"): Gets the value for parser

readData

signature(object = "pubRepo"): Reads data using readLines from a data source defined by srcUrl

srcUrl<-

signature(object = "pubRepo"): Sets the value for srcUrl

srcUrl

signature(object = "pubRepo"): Gets the value for srcUrl

Note

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

Author(s)

Jianhua Zhang

See Also

GO-class, KEGG-class, LL-class, UG-class, GEO-class

Examples

# Read a short test file from Bioconductor
test <- pubRepo(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/TGene.txt")
data <- readData(test)