[Qpcr-commits] r124 - in pkg/ReadqPCR: R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 22 11:34:24 CEST 2010
Author: jperkins
Date: 2010-09-22 11:34:23 +0200 (Wed, 22 Sep 2010)
New Revision: 124
Modified:
pkg/ReadqPCR/R/qPCRbatch.R
pkg/ReadqPCR/R/taqmanbatch.R
pkg/ReadqPCR/inst/doc/ReadqPCR.Rnw
pkg/ReadqPCR/man/ReadqPCR-package.Rd
pkg/ReadqPCR/man/qPCRBatch-class.Rd
pkg/ReadqPCR/man/read.qPCR.Rd
pkg/ReadqPCR/man/read.taqman.Rd
Log:
Almost finished ReadqPCR, need to get friend to check vignette
Modified: pkg/ReadqPCR/R/qPCRbatch.R
===================================================================
--- pkg/ReadqPCR/R/qPCRbatch.R 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/R/qPCRbatch.R 2010-09-22 09:34:23 UTC (rev 124)
@@ -1,4 +1,3 @@
-
read.qPCR <- function(filename = character(0), phenoData = new("AnnotatedDataFrame"), notes = "", verbose = FALSE)
{
pdata <- pData(phenoData)
@@ -6,8 +5,7 @@
qPCRInfo <- .read.qPCR(filename, verbose) # need to make this work for tech reps and multiple files
exprs <- qPCRInfo$exprs
well.order <- qPCRInfo$well.order
-
-exprs.well.order <- assayDataNew("environment", exprs.well.order = exprs)
+ exprs.well.order <- assayDataNew("environment", exprs.well.order = exprs)
n <- length(colnames(exprs))
if (dim(pdata)[1] != n) { # so if we don't have a row for each sample in the pData matrix
warning("Incompatible phenoData object. Created a new one using sample name data derived from raw data.\n")
@@ -29,7 +27,6 @@
.read.qPCR <- function(filename, verbose)
{
noWellData <- FALSE
-
raw.data <- read.table(filename, header=TRUE)
if(is.null(raw.data$Well) || is.null(raw.data$PlateID)) {
noWellData <- TRUE
@@ -76,8 +73,7 @@
raw.data$PlateID[raw.data$Sample == sample],
row.names=1)
}
-
- Cts <- data.frame(raw.data$Detector[raw.data$Sample == sample], # put Cts values in a matrix
+ Cts <- data.frame(raw.data$Detector[raw.data$Sample == sample],
as.numeric(as.character(raw.data$Ct[raw.data$Sample == sample])),
row.names=1)
exprs <- data.frame(merge(exprs, Cts, by="row.names"), row.names=1)
@@ -89,11 +85,9 @@
qPCRInfo <- list()
names(exprs) <- samples
qPCRInfo$exprs <- as.matrix(exprs)
-# colnames(well.order) <- names(exprs)
if(noWellData == FALSE) {
colnames(well.order) <- names(exprs)
qPCRInfo$well.order <- well.order
-# colnames(well.order) <- names(exprs)
}
return(qPCRInfo)
}
Modified: pkg/ReadqPCR/R/taqmanbatch.R
===================================================================
--- pkg/ReadqPCR/R/taqmanbatch.R 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/R/taqmanbatch.R 2010-09-22 09:34:23 UTC (rev 124)
@@ -102,7 +102,6 @@
total.detectors <- length(allDetectors[raw.data$Sample == sample])
individual.detectors <- length(unique(allDetectors[raw.data$Sample == sample]))
tech.reps <- total.detectors/individual.detectors
-#raw.data$Detector <- as.character(raw.data$Detector) # coerce to stop funny behaviour
if ((tech.reps %% 1) != 0) { # if total number of replicates not a multiple of number of individual detectors
warning.text <- paste("Corrupt taqman file: total number of readings for sample ",
sample, " not a multiple of number of individual number of detectors")
@@ -122,7 +121,7 @@
if(verbose == TRUE) cat("we are combining files with the same detector names\n")
}
else stop("Problem combining files on detector names. Make sure detector names match for all files\n")
- }
+ }#raw.data$Detector <- as.character(raw.data$Detector) # coerce to stop funny behaviour
if(firstTimeFlag == TRUE) {
exprs <- data.frame(unique(raw.data$Detector), row.names=1) # start the exprs data frame
well.order <- data.frame(unique(raw.data$Detector), row.names=1)
Modified: pkg/ReadqPCR/inst/doc/ReadqPCR.Rnw
===================================================================
--- pkg/ReadqPCR/inst/doc/ReadqPCR.Rnw 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/inst/doc/ReadqPCR.Rnw 2010-09-22 09:34:23 UTC (rev 124)
@@ -1,5 +1,5 @@
%\VignetteIndexEntry{Functions to load RT-qPCR data into R}
-%\VignetteDepends{stats,Biobase,methods}
+%\VignetteDepends{stats,Biobase,methods}
%\VignetteKeywords{real-time, quantitative, PCR, housekeeper, reference gene, geNorm, NormFinder}
%\VignettePackage{ReadqPCR}
%
@@ -17,7 +17,7 @@
%
\markboth{\sl Package ``{\tt ReadqPCR}''}{\sl Package ``{\tt ReadPCR}''}
%
-% -------------------------------------------------------------------------------
+% ------------------------------------------------------------------------------
\newcommand{\code}[1]{{\tt #1}}
\newcommand{\pkg}[1]{{\tt "#1"}}
\newcommand{\myinfig}[2]{%
@@ -28,9 +28,9 @@
\end{center}
% \end{figure}
}
-% -------------------------------------------------------------------------------
+% ------------------------------------------------------------------------------
%
-% -------------------------------------------------------------------------------
+% ------------------------------------------------------------------------------
\begin{document}
\SweaveOpts{keep.source = TRUE, eval = TRUE, include = FALSE}
%-------------------------------------------------------------------------------
@@ -41,33 +41,67 @@
}
\maketitle
\tableofcontents
+
%-------------------------------------------------------------------------------
\section{Introduction}
-The package \pkg{ReadqPCR} contains different functions for reading qPCR data into R. Different proprietary software used for the different high throghput real-time quantitative polymerase chain reaction (RT-qPCR) systems available produce different formats of output data. ReadqPCR contains functions to read some of these different formats into R so that the data can be manipulated. It also allows the user to read their own RT-qPCR data into R.
+The package \pkg{ReadqPCR} contains different functions for reading qPCR data
+into R.
-As well as the functions to read in the data, \pkg{ReadqPCR} contains the \code{qPCRBatch} class definition.
-The data output by these RT-qPCR systems is in the form of cycle threshold, or Ct values, which represents the number of cycles of amplification needed in order to detect the expression of a given gene from a sample.
+As well as the functions to read in the data, \pkg{ReadqPCR} contains the
+\code{qPCRBatch} class definition.
+The data output by these RT-qPCR systems is in the form of cycle threshold, or
+Ct values, which represents the number of cycles of amplification needed in
+order to detect the expression of a given gene from a sample.
-ReadqPCR is designed to be complementary to 2 other R modules: QCqPCR and NormqPCR, which are intended for (respectively) the quality control and normalisation of qPCR data. It must be installed before the other two modules can be.
+\pkg{ReadqPCR} is designed to be complementary to 2 other R modules: QCqPCR and
+NormqPCR, which are intended for (respectively) the quality control and
+normalisation of qPCR data. It must be installed before the other two modules.
+
%-------------------------------------------------------------------------------
\section{read.qPCR}
-\code{read.qPCR} allows the user to read in qPCR data and populate a \code{qPCRBatch} R object (see section \code{qPCRBatch}) using their own data matrix.
-The format of the data file should be tab delimited and have the following columns, the first two of which are optional (although they should either be provided both together, or not at all):
+\code{read.qPCR} allows the user to read in qPCR data and populate a
+\code{qPCRBatch} R object (see section \code{qPCRBatch}) using their own data
+matrix.
+The format of the data file should be tab delimited and have the following
+columns, the first two of which are optional (although they should either be
+provided together, or not at all):
\begin{description}
- \item[Well] Optional, this represents the position of the detector on a given plate. This information, if given, will be used to check the plates are of the same size and will also be used in order to plot a representation of the card to look for spatial effects and other potential problems. Both Well number and Plate ID must be present to enable a plate to be plotted.
- \item[Plate ID] Optional, this is an identifier for the plate on which an experiment was performed. It is not possible to have duplicate plate IDs with the same Well number. Neither is it possible to have Plate Ids without Well numbers. Both Well number and Plate ID must be present to enable a plate to be plotted.
- \item[Sample] The sample being analysed. Each sample must contain the same detectors in order to combine and compare samples effectively and to form a valid expression set matrix.
- \item[Detector] This is the identifier for the gene being investigated. The Detectors must be identical for each sample.
- \item[Ct] This is the cycle threshold for a given detector in the corresponding sample.
+ \item[Well] Optional, this represents the position of the detector on a
+plate. This information, if given, will be used to check the plates are of the
+same size and will also be used in order to plot a representation of the card to
+look for spatial effects and other potential problems. Both Well number and
+Plate ID must be present to enable a plate to be plotted.
+ \item[Plate ID] Optional, this is an identifier for the plate on which an
+experiment was performed. It is not possible to have duplicate plate IDs with
+the same Well number. Neither is it possible to have Plate Ids without Well
+numbers. Both Well number and Plate ID must be present to enable a plate to be
+plotted.
+ \item[Sample] The sample being analysed. Each sample must contain the same
+detectors in order to combine and compare samples effectively and to form a
+valid expression set matrix.
+ \item[Detector] This is the identifier for the gene being investigated. The
+Detectors must be identical for each sample.
+ \item[Ct] This is the cycle threshold for a given detector in the
+corresponding sample.
\end{description}
-The generic function \code{read.qPCR} is called to read in the qPCR file. It is similar to the \code{read.affybatch} function of the \pkg{affy} package, in that it reads a file and automatically populates an R object, \code{qPCRBatch} described below. However it is different in that the file is user formatted. In addition, unlike \code{read.affybatch}, and also unlike the \code{read.taqman} function detailed below, only one file may be read in at a time.
+The generic function \code{read.qPCR} is called to read in the qPCR file. It is
+similar to the \code{read.affybatch} function of the \pkg{affy} package, in that
+it reads a file and automatically populates an R object, \code{qPCRBatch}
+described below. However it is different in that the file is user formatted. In
+addition, unlike \code{read.affybatch}, and also unlike the \code{read.taqman}
+function detailed below, only one file may be read in at a time.
-If \code{Well} and \code{Plate ID} information are given, then these are used to populate the \code{exprs.well.order}, a new \code{assayData} slot introduced in the \code{qPCRBatch} object, as detailed below in section \code{qPCRBatch}.
+If \code{Well} and \code{Plate ID} information are given, then these are used to
+populate the \code{exprs.well.order}, a new \code{assayData} slot introduced in
+the \code{qPCRBatch} object, as detailed below in section \code{qPCRBatch}.
-So for the \code{qPCR.example.txt} file, in directory \code{exData} of this library, which contains \code{Well} and \code{Plate ID} information, as well as the mandatory \code{Sample}, \code{Detector} and \code{Ct} information, we can read in the data as follows.
+So for the \code{qPCR.example.txt} file, in directory \code{exData} of this
+library, which contains \code{Well} and \code{Plate ID} information, as well as
+the mandatory \code{Sample}, \code{Detector} and \code{Ct} information, we can
+read in the data as follows.
<<read.qPCR>>=
library(ReadqPCR) # load the ReadqPCR library
path <- system.file("exData", package = "ReadqPCR")
@@ -75,12 +109,19 @@
qPCRBatch.qPCR <- read.qPCR(qPCR.example)
@
-\code{qPCRBatch.qPCR} will be a \code{qPCRBatch} object with an exprs and exprs.well.order, as well as a phenoData slot which gets automatically populated in the same way as when using \code{read.affybatch}. More detail is given in the \code{qPCRBatch} section below.
+\code{qPCRBatch.qPCR} will be a \code{qPCRBatch} object with an exprs and
+exprs.well.order, as well as a phenoData slot which gets automatically populated
+in the same way as when using \code{read.affybatch}. More detail is given in the
+\code{qPCRBatch} section below.
-read.qPCR can deal with technical replicates. If the same detector and sample identifier occurs more than once, the suffix \code{\_TechRep.n} is concatenated to the detector name, where $n$ in \{$1, 2...N$
-\} is the number of the replication in the total number of replicates, $N$, based on
+\code{read.qPCR} can deal with technical replicates. If the same detector and
+sample identifier occurs more than once, the suffix \code{\_TechRep.n} is
+concatenated to the detector name, where $n$ in \{$1, 2...N$
+\} is the number of the replication in the total number of replicates, $N$,
+based on
order of appearence in the qPCR data file.
-So for a qPCR file with 2 technical replicates of 8 detectors on each sample, with one sample per plate, the detector names would be amended as follows:
+So for a qPCR file with 2 technical replicates and 8 detectors per replicate,
+with one replicate per plate, the detector names would be amended as follows:
<<read.qPCR.tech.reps>>=
qPCR.example.techReps <- paste(path,"/qPCR.techReps.txt", sep = "")
@@ -89,21 +130,34 @@
@
-The reason for appending the suffix when technical replicates are encountered is in order to populate the \code{exprs} and \code{exprs.well.order} slots correctly and keep them to the \code{assayData} format.
-It also allows the decisions on how to deal with the analysis and combination of technical replicates to be controlled by the user, either using the \pkg{NormqPCR} package, or potentially some other function that takes \code{assayData} format R objects as input.
+The reason for appending the suffix when technical replicates are encountered is
+in order to populate the \code{exprs} and \code{exprs.well.order} slots
+correctly and keep them to the \code{assayData} format.
+It also allows the decisions on how to deal with the analysis and combination of
+technical replicates to be controlled by the user, either using the
+\pkg{NormqPCR} package, or potentially some other function that takes
+\code{assayData} format R objects as input.
+%-------------------------------------------------------------------------------
\section{read.taqman}
-\code{read.taqman} allows the user to read in the data output by the Sequence Detection Systems (SDS) software which is the software used to analyse the Taqman Low Density Arrays.
-This data consists of the header section, which gives some general information about the experiment, run date etc., followed by the raw Cts values detected by the software, followed by summary data about the experiment.
-\code{read.taqman} is a generic function, and is called in a way similar to the \code{read.affybatch} function of the \pkg{affy} package.
+\code{read.taqman} allows the user to read in the data output by the Sequence
+Detection Systems (SDS) software which is the software used to analyse the
+Taqman Low Density Arrays.
+This data consists of the header section, which gives some general information
+about the experiment, run date etc., followed by the raw Cts values detected by
+the software, followed by summary data about the experiment.
+\code{read.taqman} is a generic function, and is called in a way similar to the
+\code{read.affybatch} function of the \pkg{affy} package.
<<read.taqman>>=
taqman.example <- paste(path, "/example.txt", sep="")
qPCRBatch.taq <- read.taqman(taqman.example)
@
-Currently the SDS software only allows up to 10 plates to be output onto one file. read.taqman allows any number of SDS output files to be combined to make a single \code{qPCRBatch}, as long as they have matching detector identifiers.
+Currently the SDS software only allows up to 10 plates to be output onto one
+file. read.taqman allows any number of SDS output files to be combined to make a
+single \code{qPCRBatch}, as long as they have matching detector identifiers.
<<read.taqman.two>>=
path <- system.file("exData", package = "ReadqPCR")
@@ -113,12 +167,21 @@
taqman.example.second.file)
@
-SDS output will not necessarily contain plate identifiers, in which case a numeric identifier will be generated, which will increment for each plate, depending on the order of the plates within the SDS files.
-This is important for filling the \code{exprs.well.order} slot of the \code{qPCRBatch}, which is used for assessing the quality of different arrays, using the \pkg{QCqPCR} package, as explained in section \code{qPCRBatch} and in the vignette for \pkg{QCqPCR}.
+SDS output will not necessarily contain plate identifiers, in which case a
+numeric identifier will be generated, which will increment for each plate,
+depending on the order of the plates within the SDS files.
+This is important for filling the \code{exprs.well.order} slot of the
+\code{qPCRBatch}, which is used for assessing the quality of different arrays,
+using the \pkg{QCqPCR} package, as explained in section \code{qPCRBatch} and in
+the vignette for \pkg{QCqPCR}.
read.taqman can also deal with technical replicates. If the same detector and
-sample identifier occurs more than once, the suffix \code{\_TechRep.n} will be concatenated to the detector name, where $n$ in \{$1, 2...N$\} is the number of the replication in the total number of replicates $N$, based on the order of occurence in the taqman data file.
-So for a taqman file with 4 technical replicates of 96 detectors per sample, with one sample per plate, the detector names would be amended as follows:
+sample identifier occurs more than once, the suffix \code{\_TechRep.n} will be
+concatenated to the detector name, where $n$ in \{$1, 2...N$\} is the number of
+the replication in the total number of replicates $N$, based on the order of
+occurence in the taqman data file.
+So for a taqman file with 4 technical replicates of 96 detectors per sample,
+with one sample per plate, the detector names would be amended as follows:
<<read.taqman.tech.reps>>=
taqman.example.tech.reps <- paste(path,"/exampleTechReps.txt", sep = "")
@@ -126,38 +189,71 @@
rownames(exprs(qPCRBatch.taq.tech.reps))[1:8]
@
-As with read.qPCR, the motivation for appending the suffix when technical replicates are encountered is in order to populate the \code{exprs} and \code{exprs.well.order} slots correctly and keep them to the \code{assayData} format.
-Again it allows the decisions on how to deal with the analysis of technical replicates to be controlled by the user, either using the \pkg{NormqPCR} package, or otherwise.
+As with read.qPCR, the motivation for appending the suffix when technical
+replicates are encountered is in order to populate the \code{exprs} and
+\code{exprs.well.order} slots correctly and keep them to the \code{assayData}
+format.
+Again it allows the decisions on how to deal with the analysis of technical
+replicates to be controlled by the user, either using the \pkg{NormqPCR}
+package, or otherwise.
+%-------------------------------------------------------------------------------
\section{qPCRBatch}
-\code{qPCRBatch} is an S4 class, designed to store information on the Ct raw values
-which represents the relative gene expression for a given sample, phenotypic information on the different samples which enable the user to compare expression accross different conditions or cell lines, and information on the spatial location of the different detectors used to measure Ct. This is achieved by
-making qPCRBatch an an extension of eSet, which means we can recycle slots such as exprs and pData, and by introducing a new \code{assyData} slot.
-Here is an example of what a qPCRBatch looks like. note the similarity to eSet:
+\code{qPCRBatch} is an S4 class, designed to store information on the Ct raw
+values
+which represents the relative gene expression for a given sample, phenotypic
+information on the different samples which enable the user to compare expression
+accross different conditions or cell lines, and information on the spatial
+location of the different detectors used to measure Ct. This is achieved by
+making \code{qPCRBatch} an an extension of eSet, which means we can recycle
+slots such as exprs and pData, and by introducing a new \code{assyData} slot.
+Here is an example of what a \code{qPCRBatch} looks like. note the similarity to
+\code{eSet}:
<<taqman.qPCRBatch>>=
qPCRBatch.taq
@
-pData will be filled automatically if no data is given, in a way analagous to read.affybatch:
+pData will be filled automatically if no data is given, in a way analagous to
+read.affybatch:
<<taqman.pData>>=
pData(qPCRBatch.taq)
@
-However it is advantageous to use pData as this information can be read by methods and functions in the \pkg{NormqPCR} and \pkg{QCqPCR} packages.
-In addition there is a new slot, \code{exprs.well.order} which extends the \code{assayData} slot used for \code{exprs()}.
-It has the same dimensions as \code{exprs} (as every instance of \code{assayData} must), which are m rows of genes and n rows of samples.
-The cells contain further details on the position on the arrays where the different meaurements were taken.
+In addition there is a new slot, \code{exprs.well.order} which extends the
+\code{assayData} slot used for \code{exprs()}.
+It has the same dimensions as \code{exprs} (as every instance of
+\code{assayData} must).
+The cells contain further details on the position on the arrays where the
+different meaurements were taken.
-The data provided by this slot can be used in order to identify certain problems with arrays, perhaps due to spatial effects and other problems with the microfluidics technology that is used by many of these systems (see \pkg{QCqPCR} for more details).
+The data provided by this slot can be used in order to identify certain problems
+with arrays, perhaps due to spatial effects and other problems with the
+microfluidics technology that is used by many of these systems (see \pkg{QCqPCR}
+for more details).
-This is conceptually similar to the cdf file information being stored in the \code{AffyBatch} class, which contains information on the spatial layout of features on an affy chip. However it differs since it allows for different arrays within the same \code{affyBatch} object to have different layouts to each other.
-This information can be viewed using the \code{exprs.well.order()} function and is later used in the \pkg{QCqPCR} package in order to produce pseudoplots of the qPCR cards, in a method analagous to the pseudo-images produced by \pkg{affyPLM}.
+This is conceptually similar to the cdf file information being stored in the
+\code{AffyBatch} class, which contains information on the spatial layout of
+features on an affy chip. However it differs since it allows for different
+arrays within the same \code{affyBatch} object to have different layouts to each
+other.
+This information can be viewed using the \code{exprs.well.order()} function and
+is later used in the \pkg{QCqPCR} package in order to produce pseudoplots of the
+qPCR cards, in a method analagous to the pseudo-images produced by
+\pkg{affyPLM}.
-When using \code{read.taqman}, if the input file includes identifiers for the different arrays in the experiment, the identifiers will be of the format \code{<plate.id>-<plate.position>}.
-However if no names are given for the different plates, \pkg{ReadqPCR} will assign them a numeric identifier, which increments depending on the order of plates in the original file.
-When several input files are given, as in the case of SDS files, the order in which they are supplied as arguments to the \code{read.taqman} function will be mirrored in the order of the numeric identifiers for the different plates. However, to minimise confusion, we recommend the useR giving the plates their own unique identifiers where possible.
+When using \code{read.taqman}, if the input file includes identifiers for the
+different arrays in the experiment, the identifiers will be of the format
+\code{<plate.id>-<plate.position>}.
+However if no names are given for the different plates, \pkg{ReadqPCR} will
+assign them a numeric identifier, which increments depending on the order of
+plates in the original file.
+When several input files are given, as in the case of SDS files, the order in
+which they are supplied as arguments to the \code{read.taqman} function will be
+mirrored in the order of the numeric identifiers for the different plates.
+However, to minimise confusion, we recommend the useR giving the plates their
+own unique identifiers where possible.
Without plate names:
<<taqman.exprs.well.order>>=
@@ -182,9 +278,14 @@
head(exprs.well.order(qPCRBatch.taq.mixedPlateNames))
@
-If the files to be combined do not have matching detector names, or if duplicate sample or plate names are given, read.taqman will stop and give an error message.
+If the files to be combined do not have matching detector names, or if duplicate
+sample or plate names are given, read.taqman will stop and give an error
+message.
\\
-When reading in \code{qPCR} files with \code{read.qPCR}, \code{exprs.well.order} will be populated as long as \code{Well} and \code{Plate ID} columns are given in the input file, otherwise the \code{exprs.well.order} slot will be \code{NULL}.
+When reading in \code{qPCR} files with \code{read.qPCR}, \code{exprs.well.order}
+will be populated as long as \code{Well} and \code{Plate ID} columns are given
+in the input file, otherwise the \code{exprs.well.order} slot will be
+\code{NULL}.
So when plate ID and Well data are given:
@@ -200,7 +301,13 @@
exprs.well.order(qPCRBatch.qPCR.noPlateOrWell)
@
-Once a qPCRBatch has been populated it is theoretically possible to use any tool which takes as it's input an \code{exprs} set matrix. However it is important to bear in mind the values are not raw expression values but Ct values, which means amongst other things that the values will be on the log scale, and a lower the Ct will indicate a higher expression level for a given transcript in the sample.
-Therefore we recommend the use of an algorithm such as those available in \pkg{NormqPCR} in order to calculate a more meaningful expression value. Also bear in mind that the amount is relative and is intended to be compared to another condition or tissue type in order to look for differential expression between condition; the technology is not designed to give absolute quantification.
+Once a qPCRBatch has been populated it is theoretically possible to use any tool
+which takes as it's input an \code{exprs} set matrix. However it is important to
+bear in mind the values are not raw expression values but Ct values, and a lower
+the Ct will indicate a higher expression level for a given transcript in the
+sample. Also it is important to note that when normalising, the amount is
+relative and is intended to be compared to another condition or tissue type in
+order to look for differential expression between condition; the technology is
+not designed to give absolute quantification.
\end{document}
Modified: pkg/ReadqPCR/man/ReadqPCR-package.Rd
===================================================================
--- pkg/ReadqPCR/man/ReadqPCR-package.Rd 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/man/ReadqPCR-package.Rd 2010-09-22 09:34:23 UTC (rev 124)
@@ -12,7 +12,7 @@
Type: \tab Package\cr
Version: \tab 1.0\cr
Date: \tab 20010-05-22\cr
-Depends: \tab R(>= 2.10.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
+Depends: \tab R(>= 2.11.0), Biobase, ReadqPCR, methods, RColorBrewer\cr
License: \tab LGPL-3\cr
LazyLoad: \tab yes\cr
}
Modified: pkg/ReadqPCR/man/qPCRBatch-class.Rd
===================================================================
--- pkg/ReadqPCR/man/qPCRBatch-class.Rd 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/man/qPCRBatch-class.Rd 2010-09-22 09:34:23 UTC (rev 124)
@@ -9,28 +9,63 @@
\alias{exprs.well.order,qPCRBatch-method}
\alias{exprs.well.order<-,qPCRBatch-method}
\title{
- Class to Contain and Describe normalise qPCR Data
+ Class qPCRBatch
}
\description{
- Container for normalised qPCR Data
+ Class to Contain and Describe raw and normalised qPCR Data, as Ct or delta-Ct values. Extends eSet
}
\section{Creating Objects}{
\code{new("qPCRBatch")}
}
-%\section{Slots}{
-%}
+\section{Slots}{
+ \describe{
+ \item{\code{assayData}:}{ Object of class \code{AssayData} containing the raw data,
+ which will be at minimum a matrix of Ct values. This
+ slot can also hold a matrix of well.info values if these are present in the input file read
+ in by \code{read.qPCR} or \code{read.taqman}
+ }
+ \item{\code{phenoData}:}{Object of class \code{AnnotatedDataFrame}
+ containing phenotypic data for the samples.
+ }
+ \item{\code{annotation}}{A character string identifying the
+ annotation that may be used for the \code{ExpressionSet}
+ instance.
+ }
+ \item{\code{protocolData}:}{Object of class \code{AnnotatedDataFrame}
+ containing protocol data for the samples.
+ }
+ \item{\code{featureData}}{Object of class \code{AnnotatedDataFrame}
+ containing feature-level (e.g., probeset-level) information.
+ }
+ \item{\code{experimentData}:}{Object of class "MIAME" containing
+ experiment-level information.
+ }
+ \item{\code{.__classVersion__}:}{Object of class \code{Versions}
+ describing the R and Biobase version number used to create the
+ instance. Intended for developer use.
+ }
+ }
+}
\section{Methods}{
\describe{
- \item{exprs.well.order}{(qPCRBatch): ... }
- \item{exprs.well.order<-}{(qPCRBatch): ... }
+ \item{exprs}{\code{signature(object = "qPCRBatch")}: extracts the Ct
+ expression matrix.}
+ \item{exprs<-}{\code{signature(object = "qPCRBatch", value = "matrix")}:
+ replaces the Ct expression matrix.}
+ \item{exprs.well.order}{\code{signature(object = "qPCRBatch")}: extracts the Ct
+ well order matrix (if it exists).}
+ \item{exprs.well.order<-}{\code{signature(object = "qPCRBatch", value = "matrix")}:
+ replaces the Ct well order matrix.}
}
}
+\note{This class is better described in the vignette.}
+\seealso{
+ \code{\link[Biobase:class.eSet]{eSet}}
+}
\author{James Perkins}
-%\examples{
-%}
\keyword{classes}
Modified: pkg/ReadqPCR/man/read.qPCR.Rd
===================================================================
--- pkg/ReadqPCR/man/read.qPCR.Rd 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/man/read.qPCR.Rd 2010-09-22 09:34:23 UTC (rev 124)
@@ -21,13 +21,24 @@
\item{verbose}{verbosity flag.}
}
\details{
- Reads a qPCR data file formatted to specifications in the ReadqPCR vignette
+ Permits the user to read in qPCR Ct value data in a predefined format
+ (more details on this format in the \code{ReadqPCR} package vignette), alongside
+ phenotypic data and further notes about the data. If \code{phenoData} is a \code{data.frame},
+ it is converted to an \code{AnnotatedDataFrame}. If it is \code{NULL} then a default object
+ of class \code{AnnotatedDataFrame} is created, whose \code{pData} is a
+ \code{data.frame} with rownames being the names of the CEL files, and
+ with one column \code{sample} with an integer index.
+ More details on how technical replicates are handled in the \code{ReadqPCR} package vignette
}
-\value{Object of class \code{"ExpressionSet"}.}
+\value{Object of class \code{"qPCRBatch"}.}
%\references{ ~put references to the literature/web site here ~ }
\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk} }
-%\note{}
+%\note{
+%}
\seealso{ \code{\link[Biobase]{ExpressionSet-class}} }
-%\examples{
-%}
+\examples{
+ path <- system.file("exData", package = "ReadqPCR")
+ qPCR.example <- paste(path, "/qPCR.example.txt", sep="")
+ qPCRBatch.qPCR <- read.qPCR(qPCR.example)
+}
\keyword{classes}
Modified: pkg/ReadqPCR/man/read.taqman.Rd
===================================================================
--- pkg/ReadqPCR/man/read.taqman.Rd 2010-09-09 17:35:35 UTC (rev 123)
+++ pkg/ReadqPCR/man/read.taqman.Rd 2010-09-22 09:34:23 UTC (rev 124)
@@ -17,19 +17,36 @@
\arguments{
\item{\dots}{file names separated by comma.}
\item{filenames}{file names in a character vector.}
- \item{phenoData}{an \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}}
- object, a \code{character} of length one, or a \code{data.frame}.}
+ \item{phenoData}{an
+ \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}}
+ object, a \code{character} of length one, or a \code{data.frame}.}
\item{notes}{notes.}
\item{verbose}{verbosity flag.}
}
\details{
- Reads a single Taqman data file.
+ Permits the user to read in qPCR Ct value data from an sds output file,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/qpcr -r 124
More information about the Qpcr-commits
mailing list