GOPkgBuilder {AnnBuilder}R Documentation

Functions to build a data package using GO data

Description

These functions creates data, documentation, and other supporting files that consist an annotation data package using data from GO.

Usage

GOPkgBuilder(pkgName = "GO", pkgPath, version = "1.6.2", go = GO(srcUrl
= getSrcUrl("GO", xml = TRUE), fromWeb = TRUE), ll = LL(srcUrl =
getSrcUrl("ll"), parser = file.path(.path.package("AnnBuilder"),
"scripts", "llNGOParser"), fromWeb = TRUE), author = list(author =
"anonymous", maintainer = "anonymous@email.com"), repList =
getRepList("go", list(ll = ll, go = go)))
writeDocs(baseName, pkgName, pkgPath, version, author, repList, pattern,
isFile = TRUE) 
copyTemplates(repList, pattern, pkgName, pkgPath, replaceBy = NULL)
getRepList(what, srcObjs)
appendObsolete(goData)
getGOTermsList(goTerms, objOK = FALSE)

Arguments

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
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
goData goData a matrix usually created using the readData method of a GO object
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
go go an object of the class GO
ll ll an object of the class LL
isFile isFile a boolean indicating whether baseName is a file or an R object
goTerms goTerms a vector of length 6
objOK objOK a boolean indicating whether the GOTerm environment will be written as list of GOTerms objects (TRUE) or lists (FALSE)

Details

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.

Value

This function does not return any value

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.godatabase.org

See Also

ABPkgBuilder, KEGGPkgBuilder

Examples

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)
}

[Package AnnBuilder version 1.4.21 Index]