\name{quantMatrix}
\alias{quantMatrix}
\title{Create an intensity matrix using quantification masses}
\description{
 Create an intensity matrix using quantification masses. The quantification
 masses can be specified when importing the library file or by manually
 setting its values (see example).
}
\usage{
quantMatrix(Lib, metabProfile, value = "maxint")
}
\arguments{
  \item{Lib}{A \code{tsLib} object created by \code{\link{ImportLibrary}} function.}
  \item{metabProfile}{ A \code{tsProfile} object. The final result of the package. This object is generated by
		either \code{Profile} or \code{ProfileCleanUp}.}
  \item{value}{The default method to select automatically the quantification mass, in case it is
   not given by the user. 'maxint' selects the selective mass with the highest intensity.
   'maxobs' selects the most observed mass, i.e., the one with less missing values.}
}
\value{
    An intensity matrix with metabolites as rows and samples as columns.
    The matrix has two attributes: 'quantMass' a numeric vector that contains the
    quantification masses that were selected; 'isSelMass' a logical vector that
    indicates whether a quantification mass is also a selected mass.
}
\examples{
require(TargetSearchData)
data(TargetSearchData)

# process chormatograms and get a profile
RI.path    <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
RIpath(sampleDescription) <- RI.path
refLibrary <- ImportLibrary(file.path(RI.path,"library.txt"))
refLibrary    <- medianRILib(sampleDescription, refLibrary)
corRI         <- sampleRI(sampleDescription, refLibrary, r_thres = 0.95)
peakData      <- peakFind(sampleDescription, refLibrary, corRI)
metabProfile  <- Profile(sampleDescription, refLibrary, peakData, r_thres = 0.95)

# show quant Matrix
quantMass(refLibrary)
# no quantMass have been defined yet, so are all zeros
# 0  0  0  0  0  0  0  0  0  0  0  0

# get a Matrix using use default values, ie, select the masses
# with the highest intensity 
quantMat <- quantMatrix(refLibrary, metabProfile)
quantMat

# set the quantification Masses
quantMass(refLibrary)[1:3] <- c(89,86,100)
quantMat <- quantMatrix(refLibrary, metabProfile)
quantMat

}
\author{Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig}
\seealso{ \code{\linkS4class{tsLib}}, \code{\linkS4class{tsMSdata}} }