[Qpcr-commits] r129 - in pkg/NormqPCR: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 21 15:42:21 CET 2011
Author: jperkins
Date: 2011-02-21 15:42:21 +0100 (Mon, 21 Feb 2011)
New Revision: 129
Added:
pkg/NormqPCR/R/allGenerics.R
pkg/NormqPCR/man/plotDCt.Rd
pkg/NormqPCR/man/plotDdCt.Rd
Modified:
pkg/NormqPCR/R/deltaCt.R
pkg/NormqPCR/R/deltaDeltaCt.R
pkg/NormqPCR/R/plotDdCt.R
pkg/NormqPCR/man/deltaCt.Rd
pkg/NormqPCR/man/deltaDeltaCt.Rd
Log:
Added file for generics and changed definitions. Also added extra help files. Still a warning in compilation of NormqPCR, because I don't know where to put the extra arguments for the deltaCt and deltaDeltaCt methods instead of using elipsis (...)
Added: pkg/NormqPCR/R/allGenerics.R
===================================================================
--- pkg/NormqPCR/R/allGenerics.R (rev 0)
+++ pkg/NormqPCR/R/allGenerics.R 2011-02-21 14:42:21 UTC (rev 129)
@@ -0,0 +1,9 @@
+setGeneric("deltaCt",
+ function(qPCRBatch, ...)
+ standardGeneric("deltaCt")
+)
+
+setGeneric("deltaDeltaCt",
+ function(qPCRBatch, ...)
+ standardGeneric("deltaDeltaCt")
+)
Modified: pkg/NormqPCR/R/deltaCt.R
===================================================================
--- pkg/NormqPCR/R/deltaCt.R 2011-02-15 17:59:59 UTC (rev 128)
+++ pkg/NormqPCR/R/deltaCt.R 2011-02-21 14:42:21 UTC (rev 129)
@@ -1,9 +1,5 @@
-setGeneric("deltaCt",
- function(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
- standardGeneric("deltaCt")
-)
setMethod("deltaCt", signature = "qPCRBatch", definition =
- function(qPCRBatch, hkgs, combineHkgs, calc) {
+ function(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith") {
hkgs <- make.names(hkgs)
# cat("hkgs",hkgs)
if(FALSE %in% (hkgs %in% featureNames(qPCRBatch))) stop ("given housekeeping gene, ", hkgs," not found in file. Ensure entered housekeeping genes appear in the file")
Modified: pkg/NormqPCR/R/deltaDeltaCt.R
===================================================================
--- pkg/NormqPCR/R/deltaDeltaCt.R 2011-02-15 17:59:59 UTC (rev 128)
+++ pkg/NormqPCR/R/deltaDeltaCt.R 2011-02-21 14:42:21 UTC (rev 129)
@@ -1,9 +1,5 @@
-setGeneric("deltaDeltaCt",
- function(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
- standardGeneric("deltaDeltaCt")
-)
setMethod("deltaDeltaCt", signature = "qPCRBatch", definition =
- function(qPCRBatch, maxNACase, maxNAControl, hkgs, contrastM, case, control, paired, hkgCalc, statCalc) {
+ function(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, case, control, paired=TRUE, hkgCalc="arith", statCalc="arith") {
hkgs <- make.names(hkgs)
# if(combineHkgs == TRUE) {
Modified: pkg/NormqPCR/R/plotDdCt.R
===================================================================
--- pkg/NormqPCR/R/plotDdCt.R 2011-02-15 17:59:59 UTC (rev 128)
+++ pkg/NormqPCR/R/plotDdCt.R 2011-02-21 14:42:21 UTC (rev 129)
@@ -1,4 +1,3 @@
-
plotDdCt <- function(..., ddCtTable, detectors="", logFC=TRUE) {
if(detectors[1]!="") {
ddCtTable <- ddCtTable[ddCtTable$ID %in% detectors, ,drop=FALSE]
Modified: pkg/NormqPCR/man/deltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaCt.Rd 2011-02-15 17:59:59 UTC (rev 128)
+++ pkg/NormqPCR/man/deltaCt.Rd 2011-02-21 14:42:21 UTC (rev 129)
@@ -6,10 +6,11 @@
Normalise qPCR eset using a given housekeeping gene as control, then perform differential expression analysis using the delta delta Ct method
}
\usage{
-deltaCt(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
+deltaCt(qPCRBatch, \dots)
}
\arguments{
\item{qPCRBatch}{ Expression set containing qPCR data. }
+ \item{\dots}{ Extra arguments, detailed below }
\item{hkgs}{ String containing the name of the name of the housekeeping gene which will be used to normalise the rest of the genes.}
\item{combineHkgs}{ Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the geometric mean. Housekeepers can be found using geNorm or NormFinder algorithms.}
\item{calc}{ use arithmetic or geometric mean.}
Modified: pkg/NormqPCR/man/deltaDeltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaDeltaCt.Rd 2011-02-15 17:59:59 UTC (rev 128)
+++ pkg/NormqPCR/man/deltaDeltaCt.Rd 2011-02-21 14:42:21 UTC (rev 129)
@@ -8,10 +8,11 @@
Suitable when housekeeping genes are from same wells/sample as the other detectors
}
\usage{
-deltaDeltaCt(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
+deltaDeltaCt(qPCRBatch,\dots)
}
\arguments{
\item{qPCRBatch}{ Expression set containing qPCR data. }
+ \item{\dots}{ Extra arguments, detailed below }
\item{maxNACase}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as case. }
\item{maxNAControl}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as control. }
\item{hkgs}{ String containing the name of th name of the housekeeping gene which will be used to normalise the rest of the genes. }
Added: pkg/NormqPCR/man/plotDCt.Rd
===================================================================
--- pkg/NormqPCR/man/plotDCt.Rd (rev 0)
+++ pkg/NormqPCR/man/plotDCt.Rd 2011-02-21 14:42:21 UTC (rev 129)
@@ -0,0 +1,33 @@
+\name{plotDCt}
+\alias{plotDCt}
+\alias{plotDCt,qPCRBatch-method}
+\title{Plot delta Ct values}
+\description{
+Takes expression set of qPCR values and plots Delta Ct after subtraction of normalisation factor (NF) or housekeeper gene
+}
+\usage{
+plotDCt(..., ddCtTable, detectors="", statCalc="arith")
+}
+\arguments{
+ \item{\dots}{ Additional arguments to pass to the plot command.
+}
+ \item{ddCtTable}{ output of deltaDeltaCt.
+}
+ \item{detectors}{ The detectors to show, if left blank will show all detectors.
+}
+ \item{statCalc}{ The type of statistic to show.
+}
+
+}
+\details{
+ Takes ddCtTable output from the deltaDeltaCt() command and plots the Ct values plus variance for a given number of detectors.
+}
+\value{
+ Produces a barplot using barplot2
+}
+%\references{ }
+\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk}}
+%\note{}
+%\seealso{}
+%\examples{}
+\keyword{plot,barplot,barplot2,barchart}
Added: pkg/NormqPCR/man/plotDdCt.Rd
===================================================================
--- pkg/NormqPCR/man/plotDdCt.Rd (rev 0)
+++ pkg/NormqPCR/man/plotDdCt.Rd 2011-02-21 14:42:21 UTC (rev 129)
@@ -0,0 +1,33 @@
+\name{plotDdCt}
+\alias{plotDdCt}
+\alias{plotDdCt,qPCRBatch-method}
+\title{Plot delta Ct values}
+\description{
+Takes expression set of qPCR values and plots Delta delta Ct after subtraction of normalisation factor (NF) or housekeeper gene and normalisation by subtraction of control
+}
+\usage{
+plotDdCt(..., ddCtTable, detectors="", logFC=TRUE)
+}
+\arguments{
+ \item{\dots}{ Additional arguments to pass to the plot command.
+}
+ \item{ddCtTable}{ output of deltaDeltaCt.
+}
+ \item{detectors}{ The detectors to show, if left blank will show all detectors.
+}
+ \item{logFC}{ plot fold change or log fold change.
+}
+
+}
+\details{
+ Takes ddCtTable output from the deltaDeltaCt() command and plots the ddCt values.
+}
+\value{
+ Produces a barplot using barplot2
+}
+%\references{ }
+\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk}}
+%\note{}
+%\seealso{}
+%\examples{}
+\keyword{plot,barplot,barplot2,barchart}
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