sampleProcessing: Peak detector of netCDF samples using xcms package
In MAIT: Statistical Analysis of Metabolomic Data

Description Usage Arguments Value Author(s) Examples

sampleProcessing takes a set of netCDF files containing LC/MS sample data and performs a peak detection, retention time correction and peak grouping steps using the package xcms. A MAIT-class object is created and all the informated is saved in it.

  sampleProcessing(dataDir = NULL, 
                   snThres = 5, 
                   Sigma = 5/2.3548,
		   mzSlices = 0.3, 
		   retcorrMethod = "loess", 
		   groupMethod = "density", 
		   bwGroup = 3, 
		   mzWidGroup = 0.25,
		   filterMethod = "centWave",
		   prefilter = c(3,3000),
  		   rtStep = 0.03, 
		   nSlaves = 0, 
		   minfrac = 0.5,
                   minsamp = 1, 
		   peakwidth = c(5, 20), 
		   project = NULL, 
		   ppm = 10,
                   family = c("gaussian", "symmetric"),
                   span = 0.2,
                   fwhm = 30)

`dataDir`	Folder where the netCDF files are stored. The samples files must be classified in subdirectories according to their classes.
`snThres`	Signal to noise ratio. Setting a high value of this parameter will lead to a higher number of features although they will be more noisy.
`Sigma`	Standard deviation (width) of matched filtration model peak.
`mzSlices`	Minimum difference in m/z for peaks with overlapping retention times.
`retcorrMethod`	Method used to correct the retention times values of the variables.
`groupMethod`	Method used to build the group peaks of variables.
`bwGroup`	Bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram.
`mzWidGroup`	Width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples.
`filterMethod`	Filtering method applied in the peak detection step.
`prefilter`	c(k, I)specifying the prefilter step for the first analysis step(ROI detection). Mass traces are only retained if they contain at least k peakswith intensity>= I.
`rtStep`	Step size to use for profile generation.
`nSlaves`	Number of slaves for parallel calculus.
`project`	Project folder name under which the results will be saved. This folder will be created in the working directory.
`minfrac`	minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group. See group.density in package xcms for details.
`minsamp`	minimum number of samples necessary in at least one of the sample groups for it to be a valid group. See group.density in package xcms for details.
`ppm`	maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million). See findPeaks.centWave in package xcms for details.
`peakwidth`	Chromatographic peak width, given as range (min,max) in seconds.
`fwhm`	See fwhm argument in xcmsSet function.
`span`	See span argument in xcmsSet function.
`family`	See family argument in xcmsSet function.

A MAIT-class object containing the data of the netCDF files. The xcmsSet-class object can be retrieved using the function rawData.

Francesc Fernandez, francesc.fernandez.albert@upc.edu

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#Provided that the data files are saved accordingly 
#in subfolders under a folder named "data" (see vignette):
#MAIT<-sampleProcessing(dataDir = "data", project = "Results", snThres=2,rtStep=0.02)

MAIT documentation built on Nov. 8, 2020, 5:43 p.m.