writeHomoXMLData {AnnBuilder} | R Documentation |
HomoloGene maintains a homology XML data file that differes both in the format and contents from the old text file version. The functions described here parse the file build the homology annotation data pacakge based on the source data.
writeHomoXMLData(pkgName = "homology", pkgPath, version, author, url = "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build39.2/homologene.xml.gz") writeHGID2Caption(pkgName, pkgPath, hgid2Cap) writeHGID2LL(pkgName, pkgPath, hgid2LL) writeHomoData(pkgName, pkgPath, homoFile) homoXMLParser(fileName)
pkgName |
pkgName a character string for the name of the
data package to be created |
pkgPath |
pkgPath a character string for the path to the
directory where the new data package will be stored |
version |
version a character string for the version
number of the data package to be created |
author |
author a list of character strings with an author
(name of the author of the data package) and a maintainer (e-mail of
the author of the package) |
url |
url a character string for the url to the ftp site
where the HomoloGene XML file is available. The url change with
different builds. Check the HomoloGene web site for the latest one |
hgid2Cap |
hgid2Cap a matrix containing mappings between
HGIDs and their textual descriptions |
hgid2LL |
hgid2LL a matrix with mappings between HGIDs and
LocusLink ids |
homoFile |
homoFile a character string for the name of a
file containing data for homologous genes |
fileName |
fileName a character string for the name of the
XML file downloaded/unzipped from HomoloGene's ftp site |
writeHomoXMLData
calls other functions listed in this
help page to complete it's tasks. All the other functions are help
functions that may not of greate interest to users.
The function returns invisible(NA)
Jianhua Zhang
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene