[Wavetiling-commits] r24 - in pkg: R inst inst/doc

[noreply at r-forge.r-project.org]

Author: kdbeuf
Date: 2012-03-01 11:34:01 +0100 (Thu, 01 Mar 2012)
New Revision: 24

Added:
   pkg/inst/NEWS.Rd
Removed:
   pkg/inst/doc/waveTiling-vignette.Rnw
Modified:
   pkg/R/allGenerics.R
   pkg/R/methods-WaveTilingFeatureSet.R
Log:
created NEWS.Rd file


Modified: pkg/R/allGenerics.R
===================================================================
--- pkg/R/allGenerics.R	2012-03-01 07:36:15 UTC (rev 23)
+++ pkg/R/allGenerics.R	2012-03-01 10:34:01 UTC (rev 24)
@@ -1,11 +1,11 @@
 # temporary(?) pmStrand
+# 
+# setGeneric("pmStrand",function(object)
+# {
+# 	standardGeneric("pmStrand")
+# }
+# )
 
-setGeneric("pmStrand",function(object)
-{
-	standardGeneric("pmStrand")
-}
-)
-
 # method data extraction
 
 setGeneric("addPheno",function(object, noGroups, groupNames, replics, ...)

Modified: pkg/R/methods-WaveTilingFeatureSet.R
===================================================================
--- pkg/R/methods-WaveTilingFeatureSet.R	2012-03-01 07:36:15 UTC (rev 23)
+++ pkg/R/methods-WaveTilingFeatureSet.R	2012-03-01 10:34:01 UTC (rev 24)
@@ -1,14 +1,14 @@
 # temporary (?)
 # I can only use this after inserting strand information to the database when parsing the bpmap and Cel file in the (updated) package PDInfoBuilder
-setMethod("pmStrand","WaveTilingFeatureSet",function(object)
-{
-	conn <- db(object)
-	sql <- paste("SELECT fid, strand", "FROM pmfeature", "INNER JOIN chrom_dict", "USING(chrom)")
-	tmp <- dbGetQuery(conn, sql)
-	tmp <- tmp[order(tmp[["fid"]]),]
-        return(tmp[["strand"]])
-}
-)
+# setMethod("pmStrand","WaveTilingFeatureSet",function(object)
+# {
+# 	conn <- db(object)
+# 	sql <- paste("SELECT fid, strand", "FROM pmfeature", "INNER JOIN chrom_dict", "USING(chrom)")
+# 	tmp <- dbGetQuery(conn, sql)
+# 	tmp <- tmp[order(tmp[["fid"]]),]
+#         return(tmp[["strand"]])
+# }
+# )
 
 
 setMethod("addPheno",signature("WaveTilingFeatureSet"),function(object,noGroups,groupNames,replics,...)

Added: pkg/inst/NEWS.Rd
===================================================================
--- pkg/inst/NEWS.Rd	                        (rev 0)
+++ pkg/inst/NEWS.Rd	2012-03-01 10:34:01 UTC (rev 24)
@@ -0,0 +1,8 @@
+\name{NEWS}
+\title{News for Package 'waveTiling'}
+
+\section{Changes in version x.y}{
+  \subsection{NEW FEATURES}{
+    \item ...;
+  }
+}

Deleted: pkg/inst/doc/waveTiling-vignette.Rnw
===================================================================
--- pkg/inst/doc/waveTiling-vignette.Rnw	2012-03-01 07:36:15 UTC (rev 23)
+++ pkg/inst/doc/waveTiling-vignette.Rnw	2012-03-01 10:34:01 UTC (rev 24)
@@ -1,51 +0,0 @@
-%\VignetteIndexEntry{The waveTiling package}
-%\VignetteDepends{}
-%\VignetteKeywords{}
-%\VignettePackage{waveTiling}
-\documentclass[10pt]{article}
-
-\usepackage{times}
-\usepackage{hyperref}
-
-\textwidth=6.5in
-\textheight=8.5in
-%\parskip=.3cm
-\oddsidemargin=-.1in
-\evensidemargin=-.1in
-\headheight=-.3in
-
-%\newcommand{\Rfunction}[1]{{\texttt{#1}}}
-%\newcommand{\Robject}[1]{{\texttt{#1}}}
-\newcommand{\Rpackage}[1]{{\textit{#1}}}
-%\newcommand{\Rmethod}[1]{{\texttt{#1}}}
-%\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
-%\newcommand{\Rclass}[1]{{\textit{#1}}}
-%\newcommand{\Rcode}[1]{{\texttt{#1}}}
-
-\newcommand{\software}[1]{\textsf{#1}}
-\newcommand{\R}{\software{R}}
-\newcommand{\waveTiling}{\Rpackage{waveTiling}}
-
-\title{The \waveTiling{} package}
-\author{Kristof De Beuf}
-\date{\today}
-
-\begin{document}
-
-\maketitle
-\tableofcontents
-
-<<options,echo=FALSE>>=
-options(width=72)
-@
-
-\section{Introduction}
-
-In this \waveTiling{} package vignette the package's main functionalities to conduct a tiling array trancriptome analysis are illustrated. The package contains an implementation of the basic wavelet-based functional model introduced in [REF] Clement et al. (2012), and its extensions towards more complex designs described in [REF] De Beuf et al. (2012). The leaf development data set [REF] (Andriankaja et al., 2012) contains genome-wide expression data measured for six developmental time points (day 8 to day 13) on the plant species \textit{Arabidopsis thaliana}. The experiment was conducted with AGRONOMICS1 tiling arrays [REF] and contains three biological replicates per time point.
-
-\section{Read in and prepare data for analysis}
-
-First we have to load the \waveTiling{} package and the \Rpackage{waveTilingData} package...
-
-
-\end{document}