SetPeakParam: Set parameters for peak profiling and parameters optimization

In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

Set parameters for peak profiling and parameters optimization

Description

This function sets all the parameters used for downstream pre-processing of user's raw MS data based on specific Liquid chromatography–mass spectrometry (LC-MS) platform or parameters optimization. The database will be under an real-time update based on the progress in this field.

Usage

SetPeakParam(
  platform = "general",
  Peak_method = "centWave",
  RT_method = "loess",
  mzdiff,
  snthresh,
  bw,
  ppm,
  min_peakwidth,
  max_peakwidth,
  noise,
  prefilter,
  value_of_prefilter,
  fwhm,
  steps,
  sigma,
  peakBinSize,
  max,
  criticalValue,
  consecMissedLimit,
  unions,
  checkBack,
  withWave,
  profStep,
  minFraction,
  minSamples,
  maxFeatures,
  mzCenterFun,
  integrate,
  extra,
  span,
  smooth,
  family,
  fitgauss,
  polarity,
  perc_fwhm,
  mz_abs_iso,
  max_charge,
  max_iso,
  corr_eic_th,
  mz_abs_add,
  adducts,
  rmConts,
  BlankSub
)

Arguments

platform	Character, specify the LC-MS platform used in pratice, including "UPLC-Q/E", "UPLC-Q/TOF","UPLC-T/TOF","UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S","HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap","HPLC-S/Q". Default is "general", which is a more common option for all platform. If the platform is not listed above, please use this one.
Peak_method	Character, specify the algorithm to perform peak detection. "centwave" to use the CentWave algorithm, and "matchedFilter" to use the MatchedFilter algorithm.
RT_method	Character, specify the algorithm to perform tetention time alignment, including "loess" and "obiwarp". Default is "loess".
mzdiff	Numeric, specify the minimum m/z difference for signals to be considered as different features when retention times are overlapping.
snthresh	Numeric, specify the signal to noise threshold. Work for both 'centwave' and 'matchedFilter'.
bw	Numeric, specify the band width (sd or half width at half maximum) of gaussian smoothing kernel to be applied during peak grouping.
ppm	Numeric, specify the mass error in ppm.
min_peakwidth	Numeric, specify the minimum peak width in seconds.Only work for 'centWave'.
max_peakwidth	Numeric, specify the maximum peak width in seconds.Only work for 'centWave'.
noise	Numeric, specify the noise level for peaking picking.Only work for 'centWave'.
prefilter	Numeric, specify the scan number threshold for prefilter.Only work for 'centWave'.
value_of_prefilter	Numeric, specify the scan abundance threshold for prefilter. Only work for 'centWave'.
fwhm	numeric specifying the full width at half maximum of matched filtration gaussian model peak. Only work for 'matchedFilter'.
steps	numeric defining the number of bins to be merged before filtration. Only work for 'matchedFilter'.
sigma	numeric specifying the standard deviation (width) of the matched filtration model peak. Only work for 'matchedFilter'.
peakBinSize	Numeric, specifying the width of the bins/slices in m/z dimension. Only work for 'matchedFilter'.
max	numeric, representing the maximum number of peaks that are expected/will be identified per slice. Only work for 'matchedFilter'.
criticalValue	criticalValue for massifquant (supported later).
consecMissedLimit	consecMissedLimit for massifquant (supported later).
unions	unions for massifquant (supported later).
checkBack	checkBack for massifquant (supported later).
withWave	withWave for massifquant (supported later). need to change.
profStep	numeric defining the bin size (in mz dimension) to be used for the profile matrix generation. Only work for 'obiwarp'.
minFraction	Numeric, specify fraction of samples in each group that contain the feature for it to be grouped.
minSamples	Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included.
maxFeatures	Numeric, specify the maximum number of features to be identified.
mzCenterFun	Character, Name of the function to calculate the m/z center of the chromatographic peak.
integrate	Integration method. For integrate = 1 peak limits are found through descent on the mexican hat filtered data, for integrate = 2 the descent is done on the real data. The latter method is more accurate but prone to noise, while the former is more robust, but less exact.
extra	Numeric, defining the maximal number of additional peaks for all samples to be assigned to a peak group (i.e. feature) for retention time correction
span	Numeric, defining the degree of smoothing (if smooth = "loess"). This parameter is passed to the internal call to loess
smooth	Character, defining the function to be used, to interpolate corrected retention times for all peak groups. Either "loess" or "linear".
family	Character, defining the method to be used for loess smoothing. Allowed values are "gaussian" and "symmetric"
fitgauss	Logical, whether or not a Gaussian should be fitted to each peak. This affects mostly the retention time position of the peak.
polarity	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
perc_fwhm	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
mz_abs_iso	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
max_charge	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
max_iso	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
corr_eic_th	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
mz_abs_add	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
adducts	PeakAnnotation parameters, (Only effective for website pipeline, for local package, OptiLCMS, please use SetAnnotationParam to define the annotation parameters).
rmConts	Logical, specify whether to exclude/remove the potential contaminations (the ones with RT range over 50% of the whole spetra).
BlankSub	Logical, to substract blanks samples or not

Value

will return a peak processing parameters' set

Author(s)

Zhiqiang Pang [e-mail], Jasmine Chong [e-mail], and Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

References

Smith, C.A. et al. 2006. Analytical Chemistry, 78, 779-787

Examples

params <- SetPeakParam(platform = "UPLC-Q/E")

xia-lab/OptiLCMS documentation built on Nov. 16, 2024, 4:36 p.m.