getSrcBuilt {AnnBuilder} | R Documentation |
Given a data source name and organism, the built date or number of the annotation source data will be returned. The built date or number is provided by the data source through its web site.
getSrcBuilt(src = "LL", organism = "Homo sapiens") getLLBuilt(url = "http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html") getUGBuilt(organism) getUCSCBuilt(organism) getGOBuilt(url = "http://www.godatabase.org/dev/database/archive/latest") getKEGGBuilt(url = "http://www.genome.jp/kegg/docs/relnote.html") getYGBuilt() getHGBuilt() getRefSeqBuilt(organism) getRefSeqBuilt() getEGBuilt()
src |
A character string for name of the data source. See details for valid names |
organism |
A character string for the name of the organism of interests. See details for valid names |
url |
A character string for the url from which built information can be obtained |
getLLBuilt
finds the built data for LocusLink from the statistics
page.
getUGBuilt
finds the built data for UniGene from the Xx.info file,
where Xx is the short organism name (e.g. Hs for human)
getUCSCBuilt
finds the built data for the Human Genome Project from
the folder for the latest release.
getGOBuilt
finds the built data for Gene Ontology from the timestamp
for the -ont.xml.gz file.
getKEGGBuilt
finds the built data for KEGG from kegg2.html page
(Release version and date)
YGBuilt
gets built information for Yeast Genome data.
Valid data source names include LL - LocusLink, UG - UniGene, UCSC - the Human Genome Project, GO - Gene Ontology, KEGG - KEGG, YG - Yeast Genome.
Valid organism name include human, mouse, rat, and yeast at this time.
All functions return a string for the built information
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua 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
## Not run: # Get built information for LocusLink ll <- getSrcBuilt(src = "LL") ug <- getSrcBuilt(src = "UG", organism = "Homo sapiens") yg <- getYGBuilt() ll ug yg ## End(Not run)