GOPkgBuilder {AnnBuilder} | R Documentation |
These functions creates data, documentation, and other supporting files that consist an annotation data package using data from GO.
GOPkgBuilder(pkgName, pkgPath, filename, version, author, lazyLoad=TRUE) writeDocs(baseName, pkgName, pkgPath, version, author, repList, pattern, isFile = TRUE) copyTemplates(repList, pattern, pkgName, pkgPath, replaceBy = NULL) getRepList(what, srcObjs)
pkgName |
pkgName a character string for the name of the
data package to be built |
pkgPath |
Describe pkgPath a character string for the path
to which the data package to be built will be stored |
filename |
Name of the GO file to parse. This file should be from the GO website in OBO XML format. |
version |
version a character string for the version
number of the data package |
author |
author a named vector of character string with a
name element for the name of the author and address element for the
email address of the author |
repList |
repList a list with LLSOURCE, GOSOURCE,
LLBUILT, GOBUILT, and DATE elements containing source url or built
date information that will be used to replace corresponding texts in
man page templates stored in the templates subdirectory |
pattern |
pattern a character string that will
be used as a pattern to copy man page templates files in the "templates"
subdirectory to the "man" subdirectory of a newly created data
package using the function copySubstitute of Biobase |
replaceBy |
replaceBy a character string specifying the
text used to replace the pattern contained by the name of a template
man page files when writing to a newly created data package |
what |
what a character string for the name of the data
package to be created for which a replacement list will be
generated |
baseName |
baseName a character string for the name of the
base file based on which a data package was built. "" if there is
none |
srcObjs |
srcObjs a list containing source data objects
that are sub classes of pubRepo |
isFile |
isFile a boolean indicating whether
baseName is a file or an R object |
lazyLoad |
lazyLoad a boolean indicating whether a lazy
load database will be created |
This package relies on the xml data file from http://www.godatabase.org/dev/database/archive/2003-04-01/go_200304-termdb.xml.gz to obtain the data. The url changes when data are updated. The system has built in code to figure out where the latest data are and use that data to build the data package.
This function does not return any value
This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
if(interactive()){ GOPkgBuilder(pkgName = "GO", pkgPath = tempdir(), version = "1.2.1", goUrl = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml", author = c(author = "who", maintainer = "who@email.com")) list.files(file.path(tempdir(), "GO")) unlink(file.path(tempdir(), "GO"), TRUE) }