[Qpcr-commits] r134 - in pkg/QCqPCR: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 28 11:09:12 CEST 2011
Author: jperkins
Date: 2011-04-28 11:09:11 +0200 (Thu, 28 Apr 2011)
New Revision: 134
Modified:
pkg/QCqPCR/DESCRIPTION
pkg/QCqPCR/NAMESPACE
pkg/QCqPCR/man/BoxWhisker.Rd
pkg/QCqPCR/man/CorMatrix.Rd
pkg/QCqPCR/man/Pairs.Rd
pkg/QCqPCR/man/PlotVsHkg.Rd
pkg/QCqPCR/man/PseudoPlot.Rd
Log:
minor changes to man files to make compilation warning free
Modified: pkg/QCqPCR/DESCRIPTION
===================================================================
--- pkg/QCqPCR/DESCRIPTION 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/DESCRIPTION 2011-04-28 09:09:11 UTC (rev 134)
@@ -5,7 +5,7 @@
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(>= 2.10.0), methods, RColorBrewer, Biobase, ReadqPCR, NormqPCR
+Depends: R(>= 2.10.0), stats, methods, RColorBrewer, Biobase, ReadqPCR, NormqPCR, gplots
License: LGPL-3
LazyLoad: yes
URL: http://qpcr.r-forge.r-project.org/
Modified: pkg/QCqPCR/NAMESPACE
===================================================================
--- pkg/QCqPCR/NAMESPACE 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/NAMESPACE 2011-04-28 09:09:11 UTC (rev 134)
@@ -1 +1,6 @@
-export(qPCRPairs, qPCRCorMatrix, plotVsHkg, PseudoPlot, qPCRBoxWhisker)
+importClassesFrom(ReadqPCR, qPCRBatch)
+export(qPCRPairs,
+ qPCRCorMatrix,
+ plotVsHkg,
+ PseudoPlot,
+ qPCRBoxWhisker)
Modified: pkg/QCqPCR/man/BoxWhisker.Rd
===================================================================
--- pkg/QCqPCR/man/BoxWhisker.Rd 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/man/BoxWhisker.Rd 2011-04-28 09:09:11 UTC (rev 134)
@@ -7,13 +7,16 @@
yet to fill
}
\usage{
-qPCRBoxWhisker(qPCRBatch, cutOff, statType, plotType)
+qPCRBoxWhisker(qPCRBatch, \dots)
+
+\S4method{qPCRBoxWhisker}{qPCRBatch}(qPCRBatch, cutOff, statType, plotType)
}
\arguments{
- \item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
- \item{cutOff}{ yet to fill }
- \item{statType}{ yet to fill }
- \item{plotType}{ yet to fill }
+ \item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
+ \item{\dots}{ Extra arguments, detailed below }
+ \item{cutOff}{ yet to fill }
+ \item{statType}{ yet to fill }
+ \item{plotType}{ yet to fill }
}
\details{ aaa
}
Modified: pkg/QCqPCR/man/CorMatrix.Rd
===================================================================
--- pkg/QCqPCR/man/CorMatrix.Rd 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/man/CorMatrix.Rd 2011-04-28 09:09:11 UTC (rev 134)
@@ -3,13 +3,14 @@
\alias{qPCRCorMatrix,qPCRBatch-method}
\title{ Make pairwise matrix of correlation values between samples in qPCR eset }
\description{
- Takes set of qPCR data and makes matrix of correlation values using pearson's coefficient
+Takes set of qPCR data and makes matrix of correlation values using pearson's coefficient
}
\usage{
qPCRCorMatrix(qPCRBatch)
+ \S4method{qPCRCorMatrix}{qPCRBatch}(qPCRBatch)
}
\arguments{
- \item{qPCRBatch}{ Expression set containing qPCR data.}
+ \item{qPCRBatch}{ Expression set containing qPCR data.}
}
\details{
reads in qPCR data and returns matrix of correlation values using Pearon's
Modified: pkg/QCqPCR/man/Pairs.Rd
===================================================================
--- pkg/QCqPCR/man/Pairs.Rd 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/man/Pairs.Rd 2011-04-28 09:09:11 UTC (rev 134)
@@ -3,17 +3,20 @@
\alias{qPCRPairs,qPCRBatch-method}
\title{ Make pairwise graphs for qPCR data from qPCR eset }
\description{
- Takes set of qPCR data and makes pairwise graphs between all the samples.
+Takes set of qPCR data and makes pairwise graphs between all the samples.
}
\usage{
-qPCRPairs(qPCRBatch, plotType = "Sample", writeToFile = FALSE, pairsToPlot = "All")
+qPCRPairs(qPCRBatch, \dots)
+
+\S4method{qPCRPairs}{qPCRBatch}(qPCRBatch, plotType = "Sample", writeToFile = FALSE, pairsToPlot = "All")
}
\arguments{
- \item{qPCRBatch}{ Expression set containing qPCR data.}
- \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"}. }
+ \item{qPCRBatch}{ Expression set containing qPCR data.}
+ \item{\dots}{ Extra arguments, detailed below }
+ \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{
generate pairwise graphs, optionally saving them to file.
Modified: pkg/QCqPCR/man/PlotVsHkg.Rd
===================================================================
--- pkg/QCqPCR/man/PlotVsHkg.Rd 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/man/PlotVsHkg.Rd 2011-04-28 09:09:11 UTC (rev 134)
@@ -3,15 +3,18 @@
\alias{plotVsHkg,qPCRBatch-method}
\title{ Plot Ct Values when normalised against different housekeeping genes }
\description{
- Takes normalised qPCR data and plot the different Ct values from the different house keeping genes
+Takes normalised qPCR data and plot the different Ct values from the different house keeping genes
}
\usage{
-plotVsHkg(qPCRBatch, hkgs, writeToFile = FALSE)
+plotVsHkg(qPCRBatch, \dots)
+
+\S4method{plotVsHkg}{qPCRBatch}(qPCRBatch, hkgs, writeToFile = FALSE)
}
\arguments{
- \item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
- \item{hkgs}{ Vector of housekeeping genes. Must all be present in the exprs matrix }
- \item{writeToFile}{ Option to write output to file }
+ \item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
+ \item{\dots}{ Extra arguments, detailed below }
+ \item{hkgs}{ Vector of housekeeping genes. Must all be present in the exprs matrix }
+ \item{writeToFile}{ Option to write output to file }
}
\details{
Takes normalised qPCR data and plot the different Ct values from the different house keeping genes.
Modified: pkg/QCqPCR/man/PseudoPlot.Rd
===================================================================
--- pkg/QCqPCR/man/PseudoPlot.Rd 2011-03-23 10:56:47 UTC (rev 133)
+++ pkg/QCqPCR/man/PseudoPlot.Rd 2011-04-28 09:09:11 UTC (rev 134)
@@ -3,19 +3,22 @@
\alias{PseudoPlot,qPCRBatch-method}
\title{ Plot Ct Values when normalised against different housekeeping genes }
\description{
- Takes normalised qPCR data and plot the different Ct values from the different house keeping genes
+Takes normalised qPCR data and plot the different Ct values from the different house keeping genes
}
\usage{
-PseudoPlot(qPCRBatch, plotType = "Cts.Values", writeToFile = FALSE,
- cutOff = NA, statType = "parametric", plateToPlot = "AllPlates")
+PseudoPlot(qPCRBatch, \dots)
+
+\S4method{PseudoPlot}{qPCRBatch}(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}{ yet to fill }
- \item{writeToFile}{ yet to fill }
- \item{cutOff}{ yet to fill }
- \item{statType}{ yet to fill }
- \item{plateToPlot}{ yet to fill }
+ \item{qPCRBatch}{ data set containing data on different Ct values normed to the different HKGs }
+ \item{\dots}{ Extra arguments, detailed below }
+ \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.
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