yeastPkgBuilder {AnnBuilder}R Documentation

Functions to do a data package for yeast genome

Description

These functions builds a data package for yeast genome using data from Yeast Genome web site of Stanford University, KEGG, and Gene Ontology.

Usage

yeastPkgBuilder(pkgName, pkgPath, base = "", srcUrls = c(YG =
                 getSrcUrl("YG"), KEGG = getSrcUrl("KEGG", organism =
                 "Saccharomyces cerevisiae"), GO = getSrcUrl("GO")),
                 version = "1.1.0",
                 makeXML = TRUE, author = list(author = "who",
                 maintainer = "who@email.com"), fromWeb = TRUE)

Arguments

pkgName pkgName a character string for the name of the data package to be built
base base a matrix with two columns with the first one being probe ids and the second one being their mappings to ORF (Open Reading Frame) ids. Columns have the name "probe" and "orf"
pkgPath pkgPath a character string for the directory where the data package to be built will be stored
srcUrls srcUrls a named vector of strings for the urls for KEGG (ftp://ftp.genome.ad.jp/pub/kegg/pathways) and GO (http://www.godatabase.org/dev/database/archive/2003-05-01/go_200305-termdb.xml.gz). The urls may change over time
version version a character string for the version number of the data package to be built
makeXML makeXML a boolean to indicate whether an XML version of the data will be generated
author author a named vector of two character strings with a name element for the name and an address element of email address of the maintainer of the data package
fromWeb fromWeb a boolean to indicate whether the data from GO should be downloaded from the web or read locally. The url for GO should be the file name of a local file if fromWeb is FALSE. For windows users, the data file from GO should be downloaded/unzipped manually and set the url for GO to be the name of the local file

Details

Annotation elements are limited to those provided by Yeast Genome (gene name, chromosome number, chromosomal location, GO id, and evidence code), KEGG (path and enzyme data) and GO (GO mappings)

Value

findYGChrLength returns a named vector of integers with chromosome numbers names and length of chromosomes as values.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.yeastgenome.org

Examples

# Not provided. 

[Package AnnBuilder version 1.4.21 Index]