MAIT (version 1.6.0)

MAITbuilder: MAIT constructor function when using external peak data

Description

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.

Usage

MAITbuilder(data = NULL,  spectraID = NULL, masses = NULL,  rt = NULL,  classes = NULL,  significantFeatures = FALSE,  spectraEstimation = FALSE,  rtRange = 0.2, corThresh = 0.7)

Arguments

data

Matrix containing the peak intensity values for each sample. Each row should correspond to a peak and each column to a sample.

spectraID

Numeric corresponding to the peak spectral grouping IDs.Two peaks having the same spectraID means that they correspond to the same spectrum.

masses

Numeric that contains the masses of the peaks. It should be as long as the number of rows in the argument data.

rt

Numeric that contains the retention time of the peaks. It should be as long as the number of rows in the argument data.

classes

Character with the class labels for each sample. It should be as long as the number of columns in the argument data.

significantFeatures

If it is set to TRUE, all the features set as an input are considered to be significant. Funcions Biotransformations, identifyMetabolites, Validation, plotPCA, plotPLS, plotHeatmap, 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.

spectraEstimation

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).

rtRange

Retention time parameter used to build a window to perform an estimation of the peak grouping into spectra.

corThresh

Peak correlation value used to define a threshhol to perform an estimation of the peak grouping into spectra.

Value

All the imput values are stored in a new MAIT object.

Examples

data(MAIT_sample)
peaks<-scores(MAIT)
aux<-getScoresTable(MAIT)
masses<-aux$extendedTable$mz
rt <- aux$extendedTable$rt
classFactor <- rep(classes(MAIT),classNum(MAIT))
importMAIT <- MAITbuilder (data=peaks,masses=masses,rt=rt,
significantFeatures=TRUE, spectraEstimation=TRUE, rtRange=0.2,
corThresh=0.7,classes=classFactor)

importMAIT