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.