%\VignetteIndexEntry{Resourcerer Resourcerer}
%\VignetteKeyword{annotation}
%\VignettePackage{Resourcerer}
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\begin{document}
\author{Jianhua Zhang}

\title{How to use Resourcerer}

\maketitle

\section{Overview}

The Gene Index Project (\url{http://compbio.dfci.harvard.edu/tgi/}, referred to as Rsouurcerer hereafter) offers
annotation data files for some commonly used Affymetrix and cDNA chips
for various organisms. The \Rpackage{Resourcerer} allows users
to either read an annotation file from Resourcerer or build an
annotation data package as the ones that are available in the MetaData
section of Bioconductor. This vignette provides instructions on how to
do both.

\section{Getting Started}
\subsection{Requirements}

The package \Rpackage{AnntationDbi} is required to perform some of the tasks
described below.

<<>>=
require("AnnotationDbi", quietly = TRUE)
require("Resourcerer", quietly = TRUE)
@

\subsection{Read annotation files from Resourcerer}

To read an annotation file from Resourcerer, one may call the function
\Rfunction(getResourcerer) by providing the name of the target file to
be read and the name of the organism the target file concerns. Please
read the help file for \Rfunction(getResourcerer) for more information
on the function and the arguments. In our example, we will try to read
a file named \verb+Agilent_Human1_cDNA.zip+, which is the annotation data
file for a cDNA chip for human located in the human subdirectory of
the root ftp site of TIGR Resourcerer.

<<>>=
agilent <- getResourcerer("Agilent_Human1_cDNA.zip", organism = "human",
destDir = file.path(path.package("Resourcerer"), "temp"), baseUrl =
            "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
            clean = TRUE )
@

The path for destDir tells \Rfunction(getResourcerer) to store the
temporary files in the temp subdirectory of \Rfunction(Resourcerer) and
clean = TRUE requests that the temporary files be removed when they are
no longer needed. The first 4 columns of the top five rows of the file
read are:

<<>>=
agilent[1:5, 1:4]
@

The full column names for \verb+Agilent_Human1_cDNA.zip+ are:

<<>>=
as.vector(colnames(agilent))
@

\subsection{Build BioC annotation data pacakges based on Resourcerer}

To build an annotation data package that is similar to the ones
available in the MetaData section of Bioconductor, one may call the
function \Rfunction(Resourcerer2BioC). In the following example, we
try to build an annotation data package for the same cDNA chip we used
before. What the function does is to subtract probe ids and the
matching public database ids (GenBank, UniGene, or Locuslink) from the
annotation file obtained from Resourcerer and then map the probe ids
to annotation data provided by other public data sources such as
LocusLink, Gene ontology, KEGG, and so on. As those annotation data are
normally very large, we only show the example code without
running. One may try the example by coping and pasting the code. It
may take up to an hour to have the sample file annotated.

<<>>=

if(interactive()) {
    resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human",
       destDir =  file.path(path.package("Resourcerer"), "temp"),
       pkgName = "AgilentHsa1",
       srcUrls = getSrcUrl("all", "Homo sapiens"),
       pkgPath =  file.path(path.package("Resourcerer"), "temp"),
       otherSrc = NULL, baseMapType = "gb",
       version = "1.1.0", fromWeb = TRUE,
       baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
               check = TRUE, author = list(authors = "Anonymous",
                              maintainer = "Anonymous <anonimous@email.com>"))
   }else{
       print("Code is executed only when invoked interactively")
   }
@

When the above code has been executed successfully, there should be a
data package named AgilentHsa1 in the temp subdirectory of
\Rpackage{Resourcerer}. The package can be used the same way as those
in the MetaData section of Bioconductor.

\end{document}