Class "YG" a sub-class of pubRepo that reads/downloads data from yeast genomic

Description

This class is a sub-class ob pubRepo that has source specific functions to extract data from Yeast Genome ftp site (ftp://genome-ftp.stanford.edu/pub/yeast/data_download/)

Objects from the Class

Objects can be created by calls of the form new("YG", ...). A constructor (YG) 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 where surce data are available (ftp://genome-ftp.stanford.edu/pub/yeast/data_download/ at the time of coding)

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 = "YG"): Reads source data defined by argument extenName from the ftp site

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

ftp://genome-ftp.stanford.edu/pub/yeast/data_download/

See Also

pubRepo-class

Examples

    # Url may change but was correct at the time of coding
    url <- "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"
    # Creat a YG object
    ygeno <- YG(srcUrl = url)
    if(interactive()){
        # Read the file named "chromosomal_feature.tab". Takes a few
        # seconds to finish
        data <- readData(ygeno,
                         "chromosomal_feature/chromosomal_feature.tab",
                         cols2Keep =c(6, 1), sep = "\t")
    }