getSrcUrl {AnnBuilder}R Documentation

Functions that find the correct url for downloading annotation data

Description

Given a source data name and organism name, the url from which the source annotation data can be downloaded will be returned.

Usage

getSrcUrl(src = "LL", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE)
getAllUrl(organism)
getLLUrl()
getUCSCUrl(organism, downloadSite = "http://hgdownload.cse.ucsc.edu/")
getUGUrl(organism)
getGOUrl(xml = TRUE, dateOnly = FALSE) 
getKEGGUrl()
readURL(url)
getGEOUrl()
getYGUrl()
getHGUrl()
getRefSeqUrl(organism)

Arguments

src A character string for the name of the data source. See details for valid names
organism A character string for the name of the organism of interests
url A character string for the url where the source data can be downloaded
dateOnly A boolean that is set to TRUE if only the built date of the data souce will be returned or TRUE if the source url will be returned
xml A boolean indicating whether the XML format data file will be downloaded/processed
downloadSite downLoadSite a character string for the url to the general downloading site for the human, mouse, and rat data

Details

getAllUrl finds the urls for all the data source including LocusLink, UinGene, the Human Geneome Project, Gene Ontology, and KEGG.

getLLUrl finds the url fro LocusLink.

getUCSCUrl finds the url for the Human Genome Project.

getUGUrl finds the url for UniGene.

getGOUrl finds the url for Gene Ontology.

getKEGGUrl finds the url for KEGG.

getGEOUrl finds the url for GOE (the CGI script)

getYGUrl gets the url to the ftp site where Yeast Genome data can be downloaded.

Valid data source names include LL - LocusLink, UG - UniGene, UCSC - the Human Genome Project, GO - Gene Ontology, KEGG - KEGG, and YG - Yeast Genome.

Valid organism name include human, mouse, rat, and yeast at this time.

Value

getAllUrl returns a vector of character strings and all the others return a character string for the url

Note

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

Author(s)

Jianhau Zhang

References

"http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html", "ftp://ftp.ncbi.nih.gov/repository/UniGene", "http://www.godatabase.org/dev/database/archive/latest", "http://www.genome.ad.jp/kegg/kegg2.html", ftp://ftp.ncbi.nih.gov/refseq/LocusLink/, http://www.yeastgenome.org

See Also

getSrcBuilt

Examples

# The source URL may be checnged or the system is down
urls <- getSrcUrl("ALL")

[Package AnnBuilder version 1.4.21 Index]