SetPeakParam: Set parameters for peak picking using XCMS and CAMERA

In simscr/metaboanalyst: 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.

Usage

SetPeakParam(
  alg = "centwave",
  ppm = 10,
  min_pkw = 10,
  max_pkw = 60,
  sn_thresh = 6,
  mzdiff = 0.01,
  bw = 5,
  min_frac = 0.5,
  min_sample_num = 1,
  max_feats = 100,
  peakgroup = FALSE,
  bin_size = 1,
  min_frac_retcor = 0.9,
  rt_filt = FALSE,
  rt_min = 200,
  rt_max = 1000
)

Arguments

alg	Character, specify the algorithm to perform peak detection. "centwave" to use the CentWave algorithm, and "match_filt" to use the MatchedFilter algorithm.
ppm	Numeric, specify the mass error in ppm.
min_pkw	Numeric, specify the minimum peak width in seconds.
max_pkw	Numeric, specify the maximum peak width in seconds.
sn_thresh	Numeric, specify the signal to noise threshold.
mzdiff	Numeric, specify the minimum m/z difference for signals to be considered as different features when retention times are overlapping.
bw	Numeric, specify the band width (sd or half width at half maximum) of gaussian smoothing kernel to be applied during peak grouping.
min_frac	Numeric, specify fraction of samples in each group that contain the feature for it to be grouped.
min_sample_num	Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included.
max_feats	Numeric, specify the maximum number of features to be identified.
peakgroup	Boolean, if true, PeakGroup algorithm is used for peak alignment; if false, Obiwarp method is used.
bin_size	Numeric, specify the bin size (in m/z) to be used for the profile matrix generation used for peak alignment (Obiwarp method).
min_frac_retcor	Numeric, specify fraction of samples in all groups that contain the peaks for them to be aligned (PeakGroup method).
rt_filt	Boolean, if true, users must specify the minimum and maximum retention time to be included in the analysis. By default this is set to 200 - 1000.
rt_min	Numeric, specify the minimum retention time.
rt_max	Numeric, specify the maximum retention time.

Author(s)

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

simscr/metaboanalyst documentation built on Jan. 21, 2020, 12:13 a.m.