[Qpcr-commits] r130 - in pkg: NormqPCR NormqPCR/man QCqPCR QCqPCR/man ReadqPCR ReadqPCR/man

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

Author: stamats
Date: 2011-02-22 20:50:14 +0100 (Tue, 22 Feb 2011)
New Revision: 130

Modified:
   pkg/NormqPCR/DESCRIPTION
   pkg/NormqPCR/man/NormqPCR-package.Rd
   pkg/NormqPCR/man/deltaCt.Rd
   pkg/NormqPCR/man/deltaDeltaCt.Rd
   pkg/QCqPCR/DESCRIPTION
   pkg/QCqPCR/man/QCqPCR-package.Rd
   pkg/ReadqPCR/DESCRIPTION
   pkg/ReadqPCR/man/ReadqPCR-package.Rd
Log:
some minor updates

Modified: pkg/NormqPCR/DESCRIPTION
===================================================================
--- pkg/NormqPCR/DESCRIPTION	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/NormqPCR/DESCRIPTION	2011-02-22 19:50:14 UTC (rev 130)
@@ -1,6 +1,6 @@
 Package: NormqPCR
 Version: 1.0
-Date: 2010-05-22
+Date: 2011-02-22
 Title: Functions for normalisation of RT-qPCR data
 Description: Functions for normalisation of real-time quantitative PCR data
 Author: Matthias Kohl, James Perkins

Modified: pkg/NormqPCR/man/NormqPCR-package.Rd
===================================================================
--- pkg/NormqPCR/man/NormqPCR-package.Rd	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/NormqPCR/man/NormqPCR-package.Rd	2011-02-22 19:50:14 UTC (rev 130)
@@ -13,7 +13,7 @@
 Package: \tab NormqPCR\cr
 Type: \tab Package\cr
 Version: \tab 1.0\cr
-Date: \tab 2010-05-22\cr
+Date: \tab 2011-02-22\cr
 Depends: \tab R(>= 2.10.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, gplots\cr
 License: \tab LGPL-3\cr
 LazyLoad: \tab yes \cr

Modified: pkg/NormqPCR/man/deltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaCt.Rd	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/NormqPCR/man/deltaCt.Rd	2011-02-22 19:50:14 UTC (rev 130)
@@ -1,5 +1,6 @@
 \name{deltaCt}
 \alias{deltaCt}
+\alias{deltaCt-methods}
 \alias{deltaCt,qPCRBatch-method}
 \title{ Perform normalization with a given housekeeping gene }
 \description{
@@ -7,6 +8,8 @@
 }
 \usage{
 deltaCt(qPCRBatch, \dots)
+
+\S4method{deltaCt}{qPCRBatch}(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
 }
 \arguments{
   \item{qPCRBatch}{ Expression set containing qPCR data. }

Modified: pkg/NormqPCR/man/deltaDeltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaDeltaCt.Rd	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/NormqPCR/man/deltaDeltaCt.Rd	2011-02-22 19:50:14 UTC (rev 130)
@@ -1,5 +1,6 @@
 \name{deltaDeltaCt}
 \alias{deltaDeltaCt}
+\alias{deltaDeltaCt-methods}
 \alias{deltaDeltaCt,qPCRBatch-method}
 \title{ Perform normalization and differential expression with given housekeeping gene }
 \description{
@@ -9,6 +10,9 @@
 }
 \usage{
 deltaDeltaCt(qPCRBatch,\dots)
+
+\S4method{deltaDeltaCt}{qPCRBatch}(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, 
+             case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
 }
 \arguments{
   \item{qPCRBatch}{ Expression set containing qPCR data. }

Modified: pkg/QCqPCR/DESCRIPTION
===================================================================
--- pkg/QCqPCR/DESCRIPTION	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/QCqPCR/DESCRIPTION	2011-02-22 19:50:14 UTC (rev 130)
@@ -1,11 +1,11 @@
 Package: QCqPCR
 Version: 1.0
-Date: 2010-05-22
+Date: 2011-02-22
 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(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer
+Depends: R(>= 2.10.0), methods, RColorBrewer, Biobase, ReadqPCR, NormqPCR
 License: LGPL-3
 LazyLoad: yes
 URL: http://qpcr.r-forge.r-project.org/

Modified: pkg/QCqPCR/man/QCqPCR-package.Rd
===================================================================
--- pkg/QCqPCR/man/QCqPCR-package.Rd	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/QCqPCR/man/QCqPCR-package.Rd	2011-02-22 19:50:14 UTC (rev 130)
@@ -11,8 +11,8 @@
 Package: \tab QCqPCR\cr
 Type: \tab Package\cr
 Version: \tab 1.0\cr
-Date: \tab 2010-05-22\cr
-Depends: \tab R(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
+Date: \tab 2011-02-22\cr
+Depends: \tab R(>= 2.10.0), methods, RColorBrewer, Biobase, ReadqPCR, NormqPCR\cr
 License: \tab LGPL-3\cr
 LazyLoad: \tab yes\cr
 }

Modified: pkg/ReadqPCR/DESCRIPTION
===================================================================
--- pkg/ReadqPCR/DESCRIPTION	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/ReadqPCR/DESCRIPTION	2011-02-22 19:50:14 UTC (rev 130)
@@ -1,6 +1,6 @@
 Package: ReadqPCR
 Version: 1.0
-Date: 2010-05-22
+Date: 2011-02-22
 Title: Read qPCR data
 Description: The package provides functions to read raw RT-qPCR data of different platforms.
 Author: James Perkins, Matthias Kohl

Modified: pkg/ReadqPCR/man/ReadqPCR-package.Rd
===================================================================
--- pkg/ReadqPCR/man/ReadqPCR-package.Rd	2011-02-21 14:42:21 UTC (rev 129)
+++ pkg/ReadqPCR/man/ReadqPCR-package.Rd	2011-02-22 19:50:14 UTC (rev 130)
@@ -11,8 +11,8 @@
 Package: \tab ReadqPCR\cr
 Type: \tab Package\cr
 Version: \tab 1.0\cr
-Date: \tab 20010-05-22\cr
-Depends: \tab R(>= 2.11.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
+Date: \tab 2011-01-22\cr
+Depends: \tab R(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
 License: \tab LGPL-3\cr
 LazyLoad: \tab yes\cr
 }