writeManPage: Write Help Documents
In PAnnBuilder: Protein annotation data package builder

Description Usage Arguments Details Author(s) References

Given the R environment in the data directory, these functions write help documents based on templates and stored them in the man directory.

 
getRepList(organism="", type, srcUrls="", built="", pkgName)
copyTemplates(repList, pattern, pkgName, pkgPath, replaceBy = NULL)
copyTemplates_DB(repList, pkgName, pkgPath)
writeDescription(pkgName, pkgPath, version, author, 
                 dataSrc = "public data repositories", 
                 license = "The Artistic License, Version 2.0")  
writeDescription_DB(pkgName, pkgPath, version, author, organism,
                    dataSrc = "public data repositories",
                    license = "The Artistic License, Version 2.0") 
    
writeManAnno(pkgName, pkgPath, version, author, repList, pattern) 
writeManAnno_DB(pkgName, pkgPath, version, author, repList)
writeManSQ(pkgName, pkgPath, version, author, repList)
writeManMerge(pkgName, pkgPath, version, author, repList, pattern)

`organism`	a character string for the name of the organism of concern. (eg: "Homo sapiens")
`type`	a character string for the concerned database. Possible values of type are : "sp", "trembl", "ipi", "refseq", "geneint", "intact", "mppi", "3DID", "DOMINE", "BaCelLo", "DBSubLoc", "SCOP", "HomoloGene", "InParanoid", "PeptideAtlas", "SysPTM", "SysBodyFluid", "GOA", "GO", "KEGGNAME", "PFAMNAME", "INTERPRONAME", "TAXNAME", "dName", "cross", "pSeq".
`srcUrls`	a character string or a string vector for the urls of database.
`built`	a character string for the version/release information of database.
`repList`	a named list which will replace the symbols in template file.
`pattern`	a character string of the prefix of template *.Rd file
`replaceBy`	a character string for the prefix of new *.Rd file. If replaceBy=NULL, pattern will be replaed by pkgName. Otherwise pattern will be replaed by replaceBy
`dataSrc`	a character string describing the data source
`license`	a character string describing the license of R package. It will appear in the description file.
`pkgName`	the name of the data package to be built. (e.g. "hsaSP")
`pkgPath`	a character string for the full path of an existing directory where the built backage will be stored.
`version`	a character string for the version number.
`author`	a list with named elements "authors" containing a character vector of author names and "maintainer" containing the complete character string for the maintainer field, for example, "Jane Doe <jdoe@doe.com>".

Write help document files for the package. getRepList return a list which will replace the symbols in template file.

If the name of "*.rda" file in the "data" subdirectory matchs the pattern, copyTemplates will produce a "*.rd" file in the "man" subdirectory. Related template files in the "inst/templates" subdirectory are needed for this function.

Parameter "names" gives the name of the data objects; copyTemplates_DB will produces relative "*.rd" files in the "man" subdirectory. Related template files in the "inst/templates" subdirectory are needed for this function.

writeDescription write descrption file for the environment-based annotation package.

writeDescription_DB write descrption file for the SQLite-based annotation package.

writeManAnno write help document files for the environment-based annotation package. writeManAnno_DB write help document files for the SQLite-based annotation package.

writeManSQ write help document files for the sequence data package.

writeManMerge write help document files for the merged package.

Hong Li

Zhang, J., Carey, V., Gentleman, R. (2003) An extensible application for assembling annotation for genomic data.Bioinformatics 19(1), 155-156.

PAnnBuilder documentation built on May 2, 2018, 4:07 a.m.