MAIT (version 1.6.0)

sampleProcessing: Peak detector of netCDF samples using xcms package

Description

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.

Usage

sampleProcessing(dataDir = NULL,  snThres = 2,  Sigma = 5/2.3548,
		   mzSlices = 0.3, 
		   retcorrMethod = "loess", 
		   groupMethod = "density", 
		   bwGroup = 3, 
		   mzWidGroup = 0.25,
		   filterMethod = "matchedFilter", 		   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)

Arguments

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.

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.

Value

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

Examples

#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)