Class "UG" a sub-class of pubRepo to handle data from UniGene

Description

This class is a sub-class of pubRepo that is implemented specifically to parse data from UniGene (XX.data.gz, where XX is a abbreviation for a given organism)

Objects from the Class

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

Slots

organism:

Object of class "character" a character string for the name of the organism of concern

srcUrl:

Object of class "character", from class "pubRepo" a character string for the url of the source data

parser:

Object of class "character", from class "pubRepo" a character string for the name of the file containing a segment of perl code with instructions on how the source data will be processed and output be generated

baseFile:

Object of class "character", from class "pubRepo" a character string for the name of the file that contains data 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)

Extends

Class "pubRepo", directly.

Methods

organism<-

signature(object = "UG"): Sets the value for the organism slot

organism

signature(object = "UG"): Gets the value for the organism slot

Note

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

Author(s)

Jianhua Zhang

References

www.ncbi.nlm.nih.gov/UniGene

See Also

pubRepo-class

Examples

if(interactive()){
# Parse a truncated version of Hs.data.gz from Bioconductor
path <- file.path(.path.package("pubRepo"), "data")
temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
"X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
"M16652"), ncol = 2, byrow = TRUE)
write.table(temp, "tempfile", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)  
ug <- UG(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
parser = file.path(path, "basedUGParser"), baseFile = "tempfile",
organism = "human")
data <- parseData(ug)
unlink("tempfile")
}