[med-svn] r18307 - in trunk/packages/R/r-bioc-qvalue/trunk/debian: . tests vignettes
Andreas Tille
tille at moszumanska.debian.org
Thu Oct 16 10:18:52 UTC 2014
Author: tille
Date: 2014-10-16 10:18:51 +0000 (Thu, 16 Oct 2014)
New Revision: 18307
Added:
trunk/packages/R/r-bioc-qvalue/trunk/debian/README.source
trunk/packages/R/r-bioc-qvalue/trunk/debian/examples
trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/
trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/control
trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test
trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/
trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/qvalue.Rnw
Removed:
trunk/packages/R/r-bioc-qvalue/trunk/debian/README.Debian
Modified:
trunk/packages/R/r-bioc-qvalue/trunk/debian/README.test
trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog
trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright
trunk/packages/R/r-bioc-qvalue/trunk/debian/docs
trunk/packages/R/r-bioc-qvalue/trunk/debian/rules
Log:
Fetch vignette from upstream SVN to enable reproducing pdf documentation and run test suite
Deleted: trunk/packages/R/r-bioc-qvalue/trunk/debian/README.Debian
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/README.Debian 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/README.Debian 2014-10-16 10:18:51 UTC (rev 18307)
@@ -1,13 +0,0 @@
-Bioconductor qvalue for Debian
-──────────────────────────────
-
-Debian ftpmaster has requested to remove the "binary without source"
-manual.pdf. You can find it here online:
-
- http://www.bioconductor.org/packages/release/bioc/vignettes/qvalue/inst/doc/manual.pdf
-
-besides other PDF documentation at the qvalue homepage
-
- http://www.bioconductor.org/packages/release/bioc/html/qvalue.html
-
- -- Andreas Tille <tille at debian.org> Thu, 07 Jun 2012 17:40:29 +0200
Added: trunk/packages/R/r-bioc-qvalue/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/README.source (rev 0)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/README.source 2014-10-16 10:18:51 UTC (rev 18307)
@@ -0,0 +1,6 @@
+Files: vignettes/manual.pdf
+ The manual can be created by fetching the full source via
+ svn --username readonly --password readonly co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qvalue/vignettes
+ The file qvalue.Rnw which is needed to create the manual was missing in the
+ source tarball but is provided in debian/vignettes and is used in the
+ autopkgtest to recreate the manual.
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/README.test 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/README.test 2014-10-16 10:18:51 UTC (rev 18307)
@@ -1,5 +1,8 @@
Notes on how this package can be tested.
────────────────────────────────────────
-This package can be tested by loading it into R with the command
-‘library(qvalue)’ in order to confirm its integrity.
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog 2014-10-16 10:18:51 UTC (rev 18307)
@@ -1,7 +1,12 @@
-r-bioc-qvalue (1.40.0+dfsg-1) UNRELEASED; urgency=medium
+r-bioc-qvalue (1.40.0-1) unstable; urgency=medium
* New upstream version
* cme fix dpkg-control
+ * Fetch vignette from upstream SVN to enable reproducing pdf documentation
+ and run test suite
+ * Add autopkgtest
+ * Replace README.Debian by README.source explaining how to recreate the
+ doc rather than removing it
-- Andreas Tille <tille at debian.org> Thu, 16 Oct 2014 10:57:42 +0200
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright 2014-10-16 10:18:51 UTC (rev 18307)
@@ -2,17 +2,15 @@
Upstream-Name: qvalue
Upstream-Contact: John D. Storey <jstorey at u.washington.edu>
Source: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html
-Files-Excluded:
- vignettes/manual.pdf
Files: *
-Copyright: © 2006-2012 Alan Dabney and John D. Storey
+Copyright: © 2006-2014 Alan Dabney and John D. Storey
License: LGPL
Files: debian/*
Copyright: 2008-2009 Steffen Moeller <moeller at debian.org>
2009-2011 Charles Plessy <plessy at debian.org>
- 2010-2012 Andreas Tille <tille at debian.org>
+ 2010-2014 Andreas Tille <tille at debian.org>
License: LGPL
License: LGPL
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/docs 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/docs 2014-10-16 10:18:51 UTC (rev 18307)
@@ -1 +1,3 @@
debian/README.test
+debian/tests/run-unit-test
+vignettes/manual.pdf
Added: trunk/packages/R/r-bioc-qvalue/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/examples (rev 0)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/examples 2014-10-16 10:18:51 UTC (rev 18307)
@@ -0,0 +1,2 @@
+vignettes
+debian/vignettes
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/rules 2014-10-16 09:18:34 UTC (rev 18306)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/rules 2014-10-16 10:18:51 UTC (rev 18307)
@@ -6,6 +6,10 @@
install/$(package)::
chmod 644 debian/$(package)/usr/lib/R/site-library/$(cranName)/doc/*
+# does not work but I have given up to understand cdbs - feel free to fix
+binary/$(package)::
+ chmod 644 debian/$(package)/usr/share/doc/$(package)/examples/vignettes/*
+
clean::
find . -name "*.pdf" -o -name "*.tex" -o -name "*-eps" -o -name "*.log" -o -name "*.ps" -o -name "*.txt" | xargs -r chmod -x
Added: trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/control (rev 0)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/control 2014-10-16 10:18:51 UTC (rev 18307)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
Added: trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test 2014-10-16 10:18:51 UTC (rev 18307)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+oname=qvalue
+pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
+for rnw in `ls *.[rRS]nw` ; do
+rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'`
+R --no-save <<EOT
+ Stangle("$rnw")
+ source("$rfile", echo=TRUE)
+EOT
+done
+# rm -rf *
Added: trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/qvalue.Rnw
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/qvalue.Rnw (rev 0)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/qvalue.Rnw 2014-10-16 10:18:51 UTC (rev 18307)
@@ -0,0 +1,164 @@
+% \VignetteDepends{stats}
+% \VignetteIndexEntry{qvalue Tutorial}
+% \VignetteKeywords{Significance Analysis}
+% \VignettePackage{qvalue}
+\documentclass[11pt]{article}
+
+\usepackage{epsfig}
+\usepackage{latexsym}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{amsfonts}
+\usepackage{amsxtra}
+\usepackage{graphicx,subfigure}
+\usepackage{vmargin}
+
+\newcommand{\Robject}[1]{{\texttt{#1}}}
+\newcommand{\Rfunction}[1]{{\texttt{#1}}}
+\newcommand{\Rpackage}[1]{{\texttt{#1}}}
+\newcommand{\Rclass}[1]{{\texttt{#1}}}
+\newcommand{\Rmethod}[1]{{\texttt{#1}}}
+\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
+
+\parindent 0in
+\setpapersize{USletter}
+\setmarginsrb{1truein}{0.5truein}{1truein}{0.5truein}{16pt}{30pt}{0pt}{20truept}
+\setlength{\emergencystretch}{2em}
+\begin{document}
+
+\title{Bioconductor's qvalue package}
+\author{Alan Dabney and John Storey \\
+Department of Biostatistics \\
+University of Washington \\
+email: \texttt{jstorey at u.washington.edu}}
+
+\maketitle
+\bibliographystyle{plain}
+\tableofcontents
+
+% library(tools)
+% Rnwfile <- file.path("c:/alan/biostat/storey/fdr/package/vignette", "qvalue.Rnw")
+% Sweave(Rnwfile)
+
+\section{Overview}
+
+The \Rpackage{qvalue} package contains functions for the computation and presentation of q-values for
+features from an experiment with multiple comparisons. A q-value is a measure of significance for a
+particular feature, analagous to a p-value. However, where the p-value assigns significance in terms
+of the false positive rate, the q-value assigns significance in terms of the false discovery rate. See
+\cite{storey:tibs:2003} for more detailed information.\\
+
+This document provides a tutorial for using the \texttt{qvalue} package. The package consists of four
+functions (\Rfunction{qvalue} for computing q-values from p-values, \Rfunction{qplot} for visualizing the
+results with graphs, \Rfunction{qsummary} for visualizing the results with a table, and \Rfunction{qwrite} for
+writing the output to file) and a GUI (\Rfunction{qvalue.gui}). As with any R package, detailed information
+on functions, their arguments and value, can be obtained in the help files. For instance, to view the help
+file for the function \Rfunction{qvalue} within R, type \texttt{? qvalue}. \\
+
+\section{Case study: the breast cancer dataset of Hedenfalk et al. (2001)}
+
+We demonstrate the functionality of this package using gene expression data from the breast cancer study
+of \cite{hedenfalk:etal:2001}. Comparison was made between two types of genetic mutation that are
+associated with an increased risk of breast cancer, BRCA1 and BRCA2. There were 7 and 8 cDNA arrays for
+BRCA1 and BRCA2, respectively. The example considered here is restricted to $3,170$ genes as described
+in \cite{storey:tibs:2003}. A 2-sample t-statistic was used to compare the two mutation types, gene by
+gene, and p-values were assigned by a permutation-based simulation of the null distribution. The original
+data and code for preprocessing can be found at
+
+\begin{center}
+\texttt{http://faculty.washington.edu/$\sim$jstorey/qvalue/results.html}.
+\end{center}
+
+The p-values from the BRCA1/BRCA2 analysis are included with the \Rpackage{qvalue} package as the dataset
+\texttt{hedenfalk}. To obtain the p-values, type \texttt{data(hedenfalk)}, and to view a description of
+the experiments and data, type \texttt{? hedenfalk}. We also check the length of the p-value vector and plot
+a histogram.\\
+
+<<input>>=
+library(qvalue)
+data(hedenfalk)
+length(hedenfalk)
+@
+
+<<fig=TRUE, include=FALSE>>=
+hist(hedenfalk)
+@
+
+\section{The \Rfunction{qvalue} function}
+
+The \Rfunction{qvalue} function computes q-values from the p-values of an experiment with multiple comparisons.
+We assign the output of the function call to the object \texttt{qobj} and plot a histogram of the q-values.
+
+<<>>=
+qobj <- qvalue(hedenfalk)
+@
+
+<<fig=TRUE, include=FALSE>>=
+hist(qobj$qvalues)
+@
+
+\section{The \Rfunction{qsummary} function}
+
+The \Rfunction{qsummary} function reports an estimate ($\pi_0$) of the proportion of genes for which the null
+hypothesis is true, and presents a table comparing p-values to q-values.
+
+<<>>=
+qsummary(qobj)
+@
+
+\section{The \Rfunction{qplot} function}
+
+The \Rfunction{qplot} function produces four plots:
+\begin{itemize}
+\item A plot of $\pi_0$ versus the tuning parameter $\lambda$ (see \cite{storey:tibs:2003}).
+\item A plot comparing p-values to q-values.
+\item A plot of the number of significant genes by q-value.
+\item A plot of the number of expected false positives by the number of significant genes.
+\end{itemize}
+
+<<fig=TRUE, include=FALSE>>=
+qplot(qobj)
+@
+
+\section{The \Rfunction{qwrite} function}
+
+The \Rfunction{qwrite} function writes the output of the function \texttt{qvalue} to a file. If all defaults
+were chosen in the call to \Rfunction{qvalue}, the output file contains $\pi_0$ in the first row and
+a $3,071 \times 2$ matrix of p- and q-values in the rest. Note that \Rfunction{qwrite} writes to the file
+``my-qvalue-results.txt'' in the working directory by default. The file name and location can be specified
+with the \Rfunarg{filename} argument to \Rfunction{qwrite}.
+
+<<>>=
+qwrite(qobj)
+@
+
+\section{The \Rfunction{qvalue.gui} GUI}
+
+The \Rfunction{qvalue.gui} function launches a GUI with which you can conduct all the tasks described above.
+The GUI is described in full detail in the accompanying manual. It is launched by typing
+\texttt{qvalue.gui()}.
+
+\bibliography{qvalue}
+
+\begin{figure}[ht]
+ \begin{center}
+ \includegraphics[width=5in,height=5in]{pHist}
+ \end{center}
+ \caption{Histogram of p-values.}
+\end{figure}
+
+\begin{figure}[ht]
+ \begin{center}
+ \includegraphics[width=5in,height=5in]{qHist}
+ \end{center}
+ \caption{Histogram of q-values.}
+\end{figure}
+
+\begin{figure}[ht]
+ \begin{center}
+ \includegraphics[width=5in,height=5in]{qPlots}
+ \end{center}
+ \caption{Miscellaneous plots.}
+\end{figure}
+
+\end{document}
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