\name{addChromaTOFPeaks}
\alias{addChromaTOFPeaks}

\title{Add ChromaTOF peak detection results}

\description{Reads ASCII tab-delimited format files (output from ChromaTOF) and attaches them to an already created \code{peaksDataset} object}

\usage{addChromaTOFPeaks(object,fns=dir(,"[Tt][Xx][Tx]"),rtDivide=60,verbose=TRUE,...)}

\arguments{

\item{object}{a \code{peaksDataset} object.}

\item{fns}{character vector of same length as \code{object@rawdata} (user ensures the order matches)}

\item{rtDivide}{number giving the amount to divide the retention times by.}

\item{verbose}{whether to give verbose output, default \code{TRUE}}

\item{...}{arguments passed on to \code{parseChromaTOF}}

}


\details{

Repeated calls to \code{parseChromaTOF} to add peak detection results to the original \code{peaksDataset} object.

}

\value{

\code{peaksDataset} object

}


\author{Mark Robinson}


\references{

Mark D Robinson (2008).  Methods for the analysis of gas chromatography - mass spectrometry data 
\emph{PhD dissertation} University of Melbourne.

}


\seealso{
\code{\link{parseChromaTOF}}, \code{\link{peaksDataset}}
}

\examples{
# need access to CDF (raw data) and ChromaTOF files 
require(gcspikelite)
gcmsPath<-paste(.find.package("gcspikelite"),"data",sep="/")

# full paths to file names
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
# [not run] cTofFiles<-dir(gcmsPath,"txt",full=TRUE)

# create a 'peaksDataset' object and add ChromaTOF peaks to it
pd<-peaksDataset(cdfFiles[1],mz=seq(50,550),rtrange=c(7.5,8.5))
# [not run] pd<-addChromTOFPeaks(pd,...)
}

\keyword{manip}