SetAnnotationParam: Set annotation parameters
In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

SetAnnotationParam

R Documentation

Set annotation parameters

Description

This function sets the parameters for peak annotation.

Usage

SetAnnotationParam(
  polarity = "positive",
  perc_fwhm = 0.6,
  mz_abs_iso = 0.005,
  max_charge = 2,
  max_iso = 2,
  corr_eic_th = 0.85,
  mz_abs_add = 0.001,
  adducts = NULL
)

Arguments

`polarity`	Character, specify the polarity of the MS instrument. Either "negative" or "positive".
`perc_fwhm`	Numeric, set the percentage of the width of the FWHM for peak grouping. Default is set to 0.6.
`mz_abs_iso`	Numeric, set the allowed variance for the search (for isotope annotation). The default is set to 0.005.
`max_charge`	Numeric, set the maximum number of the isotope charge. For example, the default is 2, therefore the max isotope charge is 2+/-.
`max_iso`	Numeric, set the maximum number of isotope peaks. For example, the default is 2, therefore the max number of isotopes per peaks is 2.
`corr_eic_th`	Numeric, set the threshold for intensity correlations across samples. Default is set to 0.85.
`mz_abs_add`	Numeric, set the allowed variance for the search (for adduct annotation). The default is set to 0.001.
`adducts`	Character, specify the adducts based on your instrument settings.

Value

will return a annotation parameter set for following annotation steps

Author(s)

Zhiqiang Pang zhiqiang.pang@mail.mcgill.ca, Jasmine Chong jasmine.chong@mail.mcgill.ca, and Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

Examples

##' Set peak annotation parameters
annParams <- SetAnnotationParam(polarity = 'positive',
                                mz_abs_add = 0.035);

##' Please check the example of PerformPeakProfiling 
##' and ExcutePlan for the whole running pipeline.

xia-lab/OptiLCMS documentation built on Nov. 26, 2024, 3:50 a.m.