\Header{writeManPage}{Functions that write supporting files needed by a data package}
\alias{escapeLatexChr}{writeManPage}
\alias{formatName}{writeManPage}
\alias{getAllRdaName}{writeManPage}
\alias{getBuild4Yeast}{writeManPage}
\alias{getDSrc}{writeManPage}
\alias{getDsrc}{writeManPage}
\alias{getExample}{writeManPage}
\alias{getItem}{writeManPage}
\alias{getSrcBuiltNRef}{writeManPage}
\alias{getSrcNBuilt}{writeManPage}
\alias{getUrlNBuilt}{writeManPage}
\alias{writeAccessory}{writeManPage}
\alias{writeDescription}{writeManPage}
\alias{writeFun}{writeManPage}
\alias{writeMan4Fun}{writeManPage}
\alias{writeMan4QC}{writeManPage}
\alias{writeREADME}{writeManPage}
\alias{writeZZZ}{writeManPage}
\keyword{manip}{writeManPage}
\begin{Description}\relax
The functions are mainly used to write man pages and supporting
functions that are needed for a data package\end{Description}
\begin{Usage}
\begin{verbatim}
writeManPage(pkgName, pkgPath, manName, organism = "human", src, isEnv =
TURE)
writeMan4Fun(pkgName, pkgPath, organism, QCList)
formatName(toFormat)
writeREADME(pkgPath, pkgName, urls)
writeDescription(pkgName, pkgPath, version, author)
getDSrc(organism)
getSrcNBuilt(dSrc, organism)
getUrlNBuilt(src, organism)
getDSrc{organism}
writeAccessory(pkgName, pkgPath, organism, version, author = c(name =
"who", address = "who@email.net"))
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)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pkgname}] A character string for the name of a data package or R
library
\item[\code{pkgName}] Same as pkgname
\item[\code{path}] A character string for the path where pkgname resides
\item[\code{pkgPath}] Same as path
\item[\code{elenames}] A vector of character strings for the name of rda
files to be produced. The names should be in the first column of
AnnInfo.rda in the data subdirectory of AnnBuilder
\item[\code{organism}] A character string for the name of the organism of
interests
\item[\code{short}] A boolean that is set to TRUE when the man page is for
rda files produced by the three functions aforementioned in which
case package name will be part of the name of the Rd files to be
produced. Otherwise, package name will not be part of the name of
the Rd files produced
\item[\code{fName}] A character string for the name of the Rd file to be
produced
\item[\code{tagName}] A character string for a Latex tag to be written to the
Rd file. Valid tags can be found in "Writing R Extensions"
\item[\code{tagCont}] A character string for the content to be written to a
Latex tag
\item[\code{toFormat}] A character string form whom any underscore will be
removed
\item[\code{urls}] A vector of character of string for the urls of the data
source used to create the rda files
\item[\code{header}] A character string for a short description of an
annotation element
\item[\code{isXML}] A boolean indicating whether header is an XML header
(TRUE) or a string (FALSE)
\item[\code{title}] A character string for the title of an Rd file that is
going to be created
\item[\code{desc}] A character string for the description of the Rd file that
is going to be created
\item[\code{keyword}] A character string for the keyword of the Rd file to be
created. The key word must be a standard R keyword
\item[\code{name}] A character string to be put in a Latex format "\item[xxx] "
where xxx = name
\item[\code{content}] A character string to be put between the "{}" following
"\item[] "
\item[\code{dSrc}] A vector of character strings containing the short names
of public data sources (e. g. LL for LocusLink)
\item[\code{src}] A character string for the short name of a public data
source
\item[\code{filename}] A character string for the name of the to write to
\item[\code{version}] A character string for the version number
\item[\code{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[\code{item}] A character string to be escaped by if it is a latex
character
\item[\code{QCList}] A list with statistical data derived from
\code{\Link{getDPStats}}
\item[\code{manName}] \code{manName} a character string for the name of the
man page to be created
\item[\code{isEnv}] \code{isEnv} a boolean to indicate whether the object a
man page concerns is an R environment or not
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
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.

\code{\Link{writeManPage}} writes a man page for a given object that
is stored in the data directory.

\code{\Link{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.

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

\code{\Link{getBuild4Yeast}} creates the text that is going to be used
for built and reference information for the man page for yeast.\end{Details}
\begin{Value}
All functions return a character string.\end{Value}
\begin{Note}\relax
The functions are part of the Bioconductor project at Dana-Farber
Cancer Institute to provide BioInformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{References}\relax
An Introduction to R - Writing R Extensions\end{References}
\begin{Examples}
\begin{ExampleCode}
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)
\end{ExampleCode}
\end{Examples}

