\Header{getDPStats}{A function to read in the statistics about a data package}
\alias{formatABQCList}{getDPStats}
\alias{getDate}{getDPStats}
\alias{getPBased}{getDPStats}
\alias{getProbeNum}{getDPStats}
\alias{matchProbes}{getDPStats}
\keyword{misc}{getDPStats}
\begin{Description}\relax
This function generates a list showing the name, data of creation,
number of genes for each rda file, and the actual number of genes that
get mapped for each rda file.\end{Description}
\begin{Usage}
\begin{verbatim}
getDPStats(baseF, pkgName, pkgPath, saveList = FALSE, isFile = TRUE)
getDate(pkgName, pkgPath, fromDesc)
getProbeNum(pkgName, pkgPath, noneNA = FALSE)
matchProbes(baseF, pkgName, pkgPath, toMatch, isFile = TRUE)
getPBased()
formatABQCList(x)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{baseF}] \code{baseF} a character string for the name of a file
that is going to be used as the base file to calculate the toatl
number of probes and matched probes by a data package
\item[\code{pkgName}] \code{pkgName} a character string for the name of the
data package of concern
\item[\code{pkgPath}] \code{pkgPath} a character string for name of the path
to which the data package is stored.
\item[\code{noneNA}] \code{nonoNA} a boolean to indicate whether counts will
exclude entries with NA as the value.
\item[\code{saveList}] \code{sageList} a boolean indicating whether the
results will be returnd as a list only (FALSE) or saved to a file as
well (TRUE)
\item[\code{toMatch}] \code{toMatch} a vector of character strings for the
names of the rda files whos keys will be matched againt the probe
ids of a base file (baseF)
\item[\code{x}] \code{x} a list object produced by function
\code{\Link{getDPStats}}
\item[\code{fromDesc}] \code{fromDesc} a boolean that will get a date from a
DESCRIPTION file if set TRUE or the current date if FALSE
\item[\code{isFile}] \code{isFile} a boolean that will be TRUE if
\code{baseF} is the name of a file
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Date of creation is the date when the package was created using
AnnBuilder and in most cases is not the date when the source file
AnnBuilder used to create the rda files was created. The date when the
source data were built are listed in the man page for the package
(?package name).

The number of genes and number of genes mapped normally differ because
not all genes in a given set can be mapped to annotation data. For
probe based rda files (maps Affymetrix ids to annotation data), the
number of mapped genes out of the total is given. For non-probe based
rda files, only the total number of mapped items is given.

The total number of probes of each rda file will be checked against
the total of the base file and the names of the rda files whose total
is off will be listed.\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{list}] A list with name and value pairs
\end{ldescription}
\end{Value}
\begin{Note}\relax
This function is 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{SeeAlso}\relax
\code{\Link{ABPkgBuilder}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Run this code after changing the settings correctly
# Change the varaibles before you run the code
pkgName <- "hgu95a"
pkgPath <- "where/your/data/package/is"
# Call getABStats
# getDPStats(pkgName, pkgPath)
\end{ExampleCode}
\end{Examples}

