writeManPage {AnnBuilder}R Documentation

Functions that write supporting files needed by a data package

Description

The functions are mainly used to write man pages and supporting functions that are needed for a data package

Usage

writeManPage(pkgName, pkgPath, manName, organism = "human", src = "ll",
isEnv = TRUE) 
writeMan4Fun(pkgName, pkgPath, organism = "human", QCList, dSrc = "all" )
formatName(toFormat)
writeREADME(pkgPath, pkgName, urls)
writeDescription(pkgName, pkgPath, version, author, dataSrc, license)
getDSrc(organism)
getSrcNBuilt(dSrc, organism)
getUrlNBuilt(src, organism)
getDSrc{organism}
writeAccessory(pkgName, pkgPath, organism, version, author = list(author =
"who", maintainer = "who@email.net"), dataSrc, license)
writeFun(pkgPath, pkgName, organism = "human")
writeZZZ(pkgPath, pkgName)
getAllRdaName(pkgName, pkgPath)
escapeLatexChr(item)
writeMan4QC(pkgName, pkgPath)
getExample(pkgName, manName, isEnv = TRUE)
getSrcBuiltNRef(src, organism)
getBuild4Yeast(src, manName)

Arguments

pkgName A character string for the name of a data package or R library
pkgPath A character string for the path where pkgname resides
organism A character string for the name of the organism of interests
toFormat A character string form whom any underscore will be removed
urls A vector of character of string for the urls of the data source used to create the rda files
dSrc A vector of character strings containing the short names of public data sources (e. g. LL for LocusLink)
src A character string for the short name of a public data source
version A character string for the version number
author A named vector of strings with two elements named name and address, respectively. Name is a character string for the name of the person who maintains the data package and address is the email address of the person
item A character string to be escaped by if it is a latex character
QCList A list with statistical data derived from getDPStats
manName manName a character string for the name of the man page to be created
isEnv isEnv a boolean to indicate whether the object a man page concerns is an R environment or not
dataSrc dataSrc a vector of character strings for the data sources used to create a package
license license a character string for the license the package is under

Details

If pkgname = "XX" and elenames = "yy", the Rd file will be "XXyy.Rd" appended to the path if short is FALSE. Otherwise, the Rd file will be "yy.Rd" appended to the path.

writeManPage writes a man page for a given object that is stored in the data directory.

getExample creates a set of example code that is going to be used in a man page depending on whether the man page is for an environment object or not.

getSrcBuiltNRef creates the text that is going to be used for built and reference information in a man page.

getBuild4Yeast creates the text that is going to be used for built and reference information for the man page for yeast.

Value

All functions return a character string.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide BioInformatics functionalities through R

Author(s)

Jianhua Zhang

References

An Introduction to R - Writing R Extensions

See Also

ABPkgBuilder

Examples

makeSrcInfo()
dir.create(file.path(".", "pkg"))
dir.create(file.path(".", "pkg", "data"))
dir.create(file.path(".", "pkg", "man"))
writeManPage("pkg", getwd(), "CHR")
list.files(file.path(getwd(), "pkg", "data"))
unlink("pkg", TRUE)

[Package AnnBuilder version 1.4.21 Index]