getSrcUrl {AnnBuilder} | R Documentation |
Given a source data name and organism name, the url from which the source annotation data can be downloaded will be returned.
getSrcUrl(src, organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE) getAllUrl(organism) getLLUrl() getUCSCUrl(organism, downloadSite) getUGUrl(organism) getGOUrl(xml = TRUE, dateOnly = FALSE) getKEGGUrl() readURL(url) getGEOUrl() getYGUrl() getHGUrl() getRefSeqUrl(organism) getEGUrl()
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 |
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.
getAllUrl
returns a vector of character strings and all the others
return a character string for the url
The functions are part of the Buiconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhau Zhang
"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