git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MAIT@95035 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 06/10/2014 23:58:52
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+\name{MAITbuilder}
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+\alias{MAITbuilder}
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+\title{MAIT constructor function when using external peak data}
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+\description{
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+Function MAITbuilder creates a MAIT-class object for a given external data. This process allows the user to analyse external peak data through all the MAIT processing steps. |
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+} |
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+\usage{
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+ |
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+MAITbuilder(data = NULL, |
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+ spectraID = NULL, |
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+ masses = NULL, |
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+ rt = NULL, |
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+ classes = NULL, |
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+ significantFeatures = FALSE, |
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+ spectraEstimation = FALSE, |
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+ rtRange = 0.2, |
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+ corThresh = 0.7) |
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+} |
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+ |
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+\arguments{
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+ \item{data}{
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+Matrix containing the peak intensity values for each sample. Each row should correspond to a peak and each column to a sample. |
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+} |
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+ \item{spectraID}{
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+Numeric corresponding to the peak spectral grouping IDs.Two peaks having the same spectraID means that they correspond to the same spectrum. |
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+} |
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+ \item{masses}{
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+Numeric that contains the masses of the peaks. It should be as long as the number of rows in the argument data. |
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+} |
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+ \item{rt}{
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+Numeric that contains the retention time of the peaks. It should be as long as the number of rows in the argument data. |
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+ } |
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+\item{classes}{
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+Character with the class labels for each sample. It should be as long as the number of columns in the argument data. |
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+ } |
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+\item{significantFeatures}{
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+If it is set to TRUE, all the features set as an input are considered to be significant. Funcions \link{Biotransformations}, \link{identifyMetabolites}, \link{Validation}, \link{plotPCA}, \link{plotPLS}, \link{plotHeatmap}, \link{plotBoxplot} are computed on the significant features only. If it is only wanted to perform an annotation process on the external peak data, this flag should be set to TRUE.
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+ } |
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+\item{spectraEstimation}{
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+If it is set to TRUE, an estimation of the peak grouping into spectra is performed. This computation is based on a retention time window (set by the argument rtRange) and a correlation threshold (defined by the parameter corThresh). |
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+} |
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+\item{rtRange}{
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+Retention time parameter used to build a window to perform an estimation of the peak grouping into spectra. |
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+} |
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+\item{corThresh}{
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+Peak correlation value used to define a threshhol to perform an estimation of the peak grouping into spectra. |
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+} |
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+ |
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+} |
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+ |
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+\value{
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+All the imput values are stored in a new MAIT object. |
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+} |
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+ |
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+\examples{
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+data(MAIT_sample) |
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+peaks<-scores(MAIT) |
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+aux<-getScoresTable(MAIT) |
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+masses<-aux$extendedTable$mz |
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+rt <- aux$extendedTable$rt |
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+classFactor <- rep(classes(MAIT),classNum(MAIT)) |
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+importMAIT <- MAITbuilder (data=peaks,masses=masses,rt=rt, |
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+significantFeatures=TRUE, spectraEstimation=TRUE, rtRange=0.2, |
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+corThresh=0.7,classes=classFactor) |
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+ |
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+importMAIT |
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+} |
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+ |
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+ |
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+\author{Francesc Fernandez,
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+ \email{[email protected]}}
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