writeHomoXMLData {AnnBuilder}R Documentation

Functions to parse HomoloGene XML data file and build the homology annotation data package

Description

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.

Usage

writeHomoXMLData(pkgName = "homology", pkgPath, version, author, url =
"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build36/homologene.xml.gz")
writeHGID2Caption(pkgName, pkgPath, hgid2Cap)
writeHGID2LL(pkgName, pkgPath, hgid2LL)
writeHomoData(pkgName, pkgPath, homoFile)
homoXMLParser(fileName)

Arguments

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

Details

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.

Value

The function returns invisible(NA)

Author(s)

Jianhua Zhang

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene

Examples



[Package AnnBuilder version 1.4.21 Index]