pubRepo-class {AnnBuilder}R Documentation

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

Description

This class provides basic functions to download/parse 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 column file with the first column being some type of arbitrary ids (e.g. Affymetrix probe ids) and the second column being the corresponding ids of a given public repository (e.g. GenBank accession numbers or UniGene ids)
built:
Object of class "character" a character string for the date or number a given source data were built
fromWeb:
Object of class "boolean" a boolean indicating whether the data will be read from a url or local file represented by srcUrl

Methods

baseFile<-
signature(object = "pubRepo"): Sets the value for baseFile
baseFile
signature(object = "pubRepo"): Gets the value for baseFile
builtInfo
signature(object = "pubRepo"): Gets the value for built
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
fromWeb
signature(object = "pubRepo"): Get the vlue for slot fromWeb
fromWeb<-
signature(object = "pubRepo"): Sets the value for slot fromWeb

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", fromWeb = TRUE)
data <- readData(test) 

[Package AnnBuilder version 1.4.21 Index]