SetPeakParam: Set parameters for peak profiling and parameters optimization

In xia-lab/MetaboAnalystR3.0: An R Package for Comprehensive Analysis of Metabolomics Data

Description

This function sets all the parameters used for downstream pre-processing of user's raw MS data based on specific 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,
  profStep,
  minFraction,
  minSamples,
  maxFeatures,
  max,
  extra,
  span,
  smooth,
  family,
  fitgauss,
  verbose.columns,
  mzCenterFun,
  integrate,
  ...
)

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.
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'.
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.
...	Other parameters, including max,extra,span,smooth,family,fitgauss, verbose.columns,mzCenterFun,integrate. Usually don't need to change.

Author(s)

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

xia-lab/MetaboAnalystR3.0 documentation built on May 6, 2020, 11:03 p.m.