#'@name read.RTqPCR
#'@aliases read.RTqPCR
#'@title To read in the raw fluorescent data of LC480 light cycler and Mx3005P RT-qPCR experiment.
#'@description Function \code{read.RTqPCR} reads in the raw fluorescent data of LC480 light cycler and Mx3005P
#'RT-qPCR and use the data to populate an object of class \code{"RTqPCRBatch"}.
#'@param file the name of the file to read in.
#'@param PCRtype the type of RT-qPCRs ("LC480" or "Mx3005P") whose file is to read in.
#'@param \dots Other parameters to be passed to downstream methods.
#'@return \code{"RTqPCRBatch"} object with exprs slots.
#'@details Function \code{read.RTqPCR} reads in the raw fluorescent data of LC480 light cycler
#'and Mx3005P RTqPCR and is based on functions \code{\link[ReadqPCR]{read.LC480}} and \code{\link{read.Mx3005P}}.
#'@author Navneet Phogat, Matthias Kohl, \email{Matthias.Kohl@@stamats.de}
#'@examples
#'##To read in the fluorescent data of LC480 light cycler
#'
#'LC480.example <- file.path(path, "LC480_Example.txt")
#'rtData.LC480 <- read.RTqPCR(LC480.example, PCRtype = "LC480")
#'rtData.LC480 ## to visualise the overview of data
#'head(exprs(rtData.LC480)) ## to visualise all of the fluorescence data
#'head(exprs(rtData.LC480[,1:5])) ## to visualise the first five columns of fluorescence data
#'head(pData(rtData.LC480)) ## to express the phenoData
#'head(fData(rtdata.LC480)) ## to express featureData
#'
#'##To read in the fluorescent data of Mx3005P RT-qPCR
#'
#'Mx3005P.example <- file.path(path, "Mx3005P_Example.txt")
#'rtData.Mx <- read.RTqPCR(Mx3005P.example, PCRtype = "Mx3005P")
#'rtData.Mx ## to visualise the overview of data
#'head(exprs(rtData.Mx)) ## to visualise all of the fluorescence data
#'head(exprs(rtData.Mx[,1:5])) ## to express the first five columns of fluorescence data
#'head(pData(rtData.Mx)) ## to express the phenoData
#'head(fData(rtData.Mx)) ## to express the featureData
#'
#'@export
read.RTqPCR <- function (file, PCRtype, ...)
{
if (PCRtype == "LC480")
{
x <- read.LC480(file = file)
x.exprs <- exprs(x)
x.featureData <- featureData(x)
x.phenoData <- phenoData(x)
cycData <- new("RTqPCRBatch", exprs = x.exprs, featureData = x.featureData, phenoData = x.phenoData)
}
else
{
if (PCRtype == "Mx3005P")
{
cycData <- read.Mx3005P(file = file)
}
else
{
stop("Define appropriate PCRtype out of LC480 or Mx3005P!")
}
}
return(cycData)
}
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