sampleProcessing {MAIT} | R Documentation |
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
#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)