UpdateInstrumentParameters: Update the mSetObj with user-selected parameters for MS Peaks...

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Update the mSetObj with user-selected parameters for MS Peaks to Pathways.

Description

This functions handles updating the mSet object for mummichog analysis. It is necessary to utilize this function to specify to the organism's pathways to use (libOpt), the mass-spec mode (msModeOpt) and mass-spec instrument (instrumentOpt).

Usage

UpdateInstrumentParameters(mSetObj=NA, instrumentOpt, 
msModeOpt, force_primary_ion, rt_frac, rt_tol)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects).
instrumentOpt	Numeric. Define the mass-spec instrument used to perform untargeted metabolomics.
msModeOpt	Character. Define the mass-spec mode of the instrument used to perform untargeted metabolomics.
force_primary_ion	Character, if "yes", only mz features that match compounds with a primary ion are kept.
rt_frac	rt_frac.
rt_tol	rt_tol.

Author(s)

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

xia-lab/MetaboAnalystR documentation built on April 20, 2024, 8:13 p.m.