[Qpcr-commits] r108 - in pkg/QCqPCR: . R inst inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat May 22 10:33:04 CEST 2010
Author: stamats
Date: 2010-05-22 10:33:04 +0200 (Sat, 22 May 2010)
New Revision: 108
Modified:
pkg/QCqPCR/DESCRIPTION
pkg/QCqPCR/R/qPCRPairs.R
pkg/QCqPCR/inst/CITATION
pkg/QCqPCR/inst/doc/QCqPCR.Rnw
pkg/QCqPCR/man/BoxWhisker.Rd
pkg/QCqPCR/man/Pairs.Rd
pkg/QCqPCR/man/PseudoPlot.Rd
pkg/QCqPCR/man/QCqPCR-package.Rd
Log:
some minor modifications/updates
Modified: pkg/QCqPCR/DESCRIPTION
===================================================================
--- pkg/QCqPCR/DESCRIPTION 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/DESCRIPTION 2010-05-22 08:33:04 UTC (rev 108)
@@ -1,11 +1,11 @@
Package: QCqPCR
Version: 1.0
-Date: 2008-10-20
+Date: 2010-05-22
Title: Functions for quality control of RT-qPCR data
Description: Functions for quality control of real-time quantitative PCR data
Author: James Perkins, Matthias Kohl
Maintainer: James Perkins <jperkins at biochem.ucl.ac.uk>
-Depends: R(>= 2.7.0), Biobase, ReadqPCR, methods, RColorBrewer
-License: GPL (>= 2)
+Depends: R(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer
+License: LGPL-3
LazyLoad: yes
URL: http://qpcr.r-forge.r-project.org/
Modified: pkg/QCqPCR/R/qPCRPairs.R
===================================================================
--- pkg/QCqPCR/R/qPCRPairs.R 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/R/qPCRPairs.R 2010-05-22 08:33:04 UTC (rev 108)
@@ -12,7 +12,7 @@
cat("HEREIHOPE\n")
pairsToPlot <- combn(pairsToPlot,2)
}
- plotMat = exprs(qPCRBatch)
+ plotMat <- exprs(qPCRBatch)
apply(pairsToPlot, 2, .plotPairs, plotMat, writeToFile)
}
else if (plotType == "Plate") {
@@ -20,8 +20,8 @@
pairsToPlot <- combn(sampleNames(qPCRBatch),2)
}
else {
- plateVec <- as.vector(gsub("-.*", "", orderMat))
- wellVec <- as.numeric(gsub(".*-", "", orderMat))
+ plateVec <- as.vector(gsub("-.*", "", pairsToPlot)) # orderMat not defined!
+ wellVec <- as.numeric(gsub(".*-", "", pairsToPlot))
plotMat <- matrix(ncol = length(levels(as.factor(plateVec))), nrow = max(wellVec))
}
for(i in plateVec) {
@@ -42,7 +42,7 @@
if (writeToFile) jpeg(filename = paste(x, "_", y, "_Pairs_Plot.jpeg", sep = ""))
# plotMat <- as.data.frame(exprs(qPCRBatch))
plot(plotMat[, x], plotMat[, y], xlab = x, ylab = y, xlim = c(1, max(plotMat[, x], na.rm=TRUE)), ylim = c(1, max(plotMat[, y], na.rm=TRUE)))
- title(main <- c(x, "vs", y, "R^2 = ", cor(plotMat[, x] ,plotMat[, y], use <- "complete.obs")))
+ title(main = paste(x, "vs", y, "R^2 = ", cor(plotMat[, x] ,plotMat[, y], use = "complete.obs")))
abline(0, 1)
if (writeToFile) dev.off()
}
Modified: pkg/QCqPCR/inst/CITATION
===================================================================
--- pkg/QCqPCR/inst/CITATION 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/inst/CITATION 2010-05-22 08:33:04 UTC (rev 108)
@@ -1,3 +1,7 @@
+if(!exists("meta") || is.null(meta)) meta <- packageDescription("QCqPCR")
+year <- sub("-.*", "", meta$Date)
+note <- sprintf("R package version %s", meta$Version)
+
citHeader("To cite package QCqPCR in publications use:")
citEntry(entry="Manual",
@@ -4,6 +8,11 @@
title = "QCqPCR: Functions for quality control of RT-qPCR data",
author = personList(as.person("J. Perkins"), as.person("M. Kohl")),
language = "English",
- year = 2008,
+ year = year,
+ note = note,
type = "R package",
-textVersion = paste("Perkins, J. and Kohl, M., (2008).", "QCqPCR: Functions for quality control of RT-qPCR data.", "R package."))
+ url = "http://qpcr.r-forge.r-project.org/",
+ textVersion = paste("Perkins, J. and Kohl, M.",
+ sprintf("(%s).", year),
+ "QCqPCR: Functions for quality control of RT-qPCR data.",
+ paste(note, ".", sep = "")))
Modified: pkg/QCqPCR/inst/doc/QCqPCR.Rnw
===================================================================
--- pkg/QCqPCR/inst/doc/QCqPCR.Rnw 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/inst/doc/QCqPCR.Rnw 2010-05-22 08:33:04 UTC (rev 108)
@@ -1,6 +1,6 @@
%\VignetteIndexEntry{QCqPCR}
%\VignetteDepends{stats,Biobase,methods,ReadqPCR}
-%\VignetteKeywords{real-time, quantitative, PCR, housekeeper, reference gene, geNorm, NormFinder}
+%\VignetteKeywords{real-time, quantitative, PCR, quality control}
%\VignettePackage{QCqPCR}
%
\documentclass[11pt]{article}
@@ -9,9 +9,9 @@
\usepackage[%
baseurl={http://qpcr.r-forge.r-project.org/},%
pdftitle={QCqPCR: Functions to assess the quality of qPCR data in R},%
-pdfauthor={Matthias Kohl and James Perkins},%
+pdfauthor={James Perkins},%
pdfsubject={QCqPCR},%
-pdfkeywords={real-time, quantitative, PCR, qPCR, RT-qPCR, housekeeper, reference gene, geNorm, NormFinder},%
+pdfkeywords={real-time, quantitative, PCR, qPCR, RT-qPCR, quality control},%
pagebackref,bookmarks,colorlinks,linkcolor=darkblue,citecolor=darkblue,%
pagecolor=darkblue,raiselinks,plainpages,pdftex]{hyperref}
%
Modified: pkg/QCqPCR/man/BoxWhisker.Rd
===================================================================
--- pkg/QCqPCR/man/BoxWhisker.Rd 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/man/BoxWhisker.Rd 2010-05-22 08:33:04 UTC (rev 108)
@@ -3,26 +3,27 @@
\alias{qPCRBoxWhisker}
\alias{qPCRBoxWhisker,qPCRBatch-method}
\title{ Box and whisker plots }
-\description{ aaa
+\description{
+ yet to fill
}
\usage{
qPCRBoxWhisker(qPCRBatch, cutOff, statType, plotType)
}
\arguments{
\item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
- \item{cutOff}{}
- \item{statType}{}
- \item{plotType}{}
+ \item{cutOff}{ yet to fill }
+ \item{statType}{ yet to fill }
+ \item{plotType}{ yet to fill }
}
\details{ aaa
}
\section{Methods}{
\describe{
- \item{qPCRBoxWhisker}{(qPCRBatch): ... }
+ \item{qPCRBoxWhisker}{(qPCRBatch): method for object of class \code{"qPCRBatch"} }
}
}
-\value{ aaa }
+\value{ yet to fill }
%\references{ ~put references to the literature/web site here ~ }
\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk} }
%\examples{
Modified: pkg/QCqPCR/man/Pairs.Rd
===================================================================
--- pkg/QCqPCR/man/Pairs.Rd 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/man/Pairs.Rd 2010-05-22 08:33:04 UTC (rev 108)
@@ -6,21 +6,24 @@
Takes set of qPCR data and makes pairwise graphs between all the samples.
}
\usage{
-qPCRPairs(qPCRBatch, writeToFile = FALSE)
+qPCRPairs(qPCRBatch, plotType = "Sample", writeToFile = FALSE, pairsToPlot = "All")
}
\arguments{
\item{qPCRBatch}{ Expression set containing qPCR data.}
- \item{writeToFile}{ Option to write to file}
+ \item{plotType}{ type of plot. So far, \code{"Sample"} and \code{"Plate"}
+ are implemented. Default is \code{"Sample"}. }
+ \item{writeToFile}{ logical, write to jpeg-file. Default is \code{FALSE}. }
+ \item{pairsToPlot}{ which pairs shall be plotted. Default is \code{"All"}. }
}
\details{
- reads in qPCR data and pairwise graphs, optionally saving them to file
+ generate pairwise graphs, optionally saving them to file.
}
\section{Methods}{
\describe{
- \item{qPCRPairs}{(qPCRBatch): ... }
+ \item{qPCRPairs}{(qPCRBatch): method for object of class \code{"qPCRBatch"}. }
}
}
-\value{produces graph and optionally writes to ping if called.}
+\value{produces graph and optionally writes to jpeg if called.}
%\references{ ~put references to the literature/web site here ~ }
\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk} }
%\examples{
Modified: pkg/QCqPCR/man/PseudoPlot.Rd
===================================================================
--- pkg/QCqPCR/man/PseudoPlot.Rd 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/man/PseudoPlot.Rd 2010-05-22 08:33:04 UTC (rev 108)
@@ -6,14 +6,16 @@
Takes normalised qPCR data and plot the different Ct values from the different house keeping genes
}
\usage{
-PseudoPlot(qPCRBatch, plotType, writeToFile, cutOff, statType)
+PseudoPlot(qPCRBatch, plotType = "Cts.Values", writeToFile = FALSE,
+ cutOff = NA, statType = "parametric", plateToPlot = "AllPlates")
}
\arguments{
\item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
- \item{plotType}{}
- \item{writeToFile}{}
- \item{cutOff}{}
- \item{statType}{}
+ \item{plotType}{ yet to fill }
+ \item{writeToFile}{ yet to fill }
+ \item{cutOff}{ yet to fill }
+ \item{statType}{ yet to fill }
+ \item{plateToPlot}{ yet to fill }
}
\details{
Takes normalised qPCR data and plot the different Ct values from the different house keeping genes.
@@ -21,7 +23,7 @@
}
\section{Methods}{
\describe{
- \item{PseudoPlot}{(qPCRBatch): ... }
+ \item{PseudoPlot}{(qPCRBatch): method for object of class \code{"qPCRBatch"} }
}
}
Modified: pkg/QCqPCR/man/QCqPCR-package.Rd
===================================================================
--- pkg/QCqPCR/man/QCqPCR-package.Rd 2010-05-22 08:12:22 UTC (rev 107)
+++ pkg/QCqPCR/man/QCqPCR-package.Rd 2010-05-22 08:33:04 UTC (rev 108)
@@ -11,8 +11,9 @@
Package: \tab QCqPCR\cr
Type: \tab Package\cr
Version: \tab 1.0\cr
-Date: \tab 2008-10-20\cr
-License: \tab GPL (>= 2)\cr
+Date: \tab 2010-05-22\cr
+Depends: \tab R(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
+License: \tab LGPL-3\cr
LazyLoad: \tab yes\cr
}
library(QCqPCR)
@@ -32,7 +33,11 @@
%~~ Optional links to other man pages, e.g. ~~
%~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
%}
-%\examples{
-%~~ simple examples of the most important functions ~~
-%}
+\examples{
+## some examples are given in the vignette
+\dontrun{
+library(QCqPCR)
+vignette("QCqPCR")
+}
+}
\keyword{ package }
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