getDefaultXcmsSetStartingParams: Creates a List of parameters for xcms-methods...

In rietho/IPO: Automated Optimization of XCMS Data Processing parameters

Creates a List of parameters for xcms-methods xcmsSet.findPeak which are optimized by default

Description

This function creates a list of parameters used in the xcmsSet.findPeak-methods 'centWave' and 'matchedFilter'. Per default the following parameters have a defined range where optimization should start:
'centWave' parameters: 'peakwidth' (split into 'min_peakwidth' and 'max_peakwidth'), 'ppm', 'mzdiff'
'matchedFilter' parameters: 'fwhm', 'snthresh', 'step', 'steps'

Usage

getDefaultXcmsSetStartingParams(method = c("centWave", "matchedFilter"))

Arguments

method

Either parameters for 'centWave' or 'matchedFilter' should be created

Details

* Do not delete a parameter from the list returned.
* Optimization of qualitative parameters is not supported yet.
* If you want to optimize additional parameter just set an lower and an upper bound (e.g. params$snthresh <- c(5,20))
* If you dont want to optimize a parameter set a default value (e.g. params$snthresh <- 10)

Value

A List of parameters for the xcmsSet.findPeak-methods 'centWave' or 'matchedFilter'

Author(s)

Gunnar Libiseller

Examples

params <- getDefaultXcmsSetStartingParams()
params$ppm <- 10
params$snthresh <- c(5,15)
params

params <- getDefaultXcmsSetStartingParams("matchedFilter")
params

rietho/IPO documentation built on Dec. 6, 2022, 8:17 a.m.