getDefaultRetGroupStartingParams: Gives a List of parameters for xcms-methods retcor.obiwarp or...

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

Gives a List of parameters for xcms-methods retcor.obiwarp or retcor.loess and group.density which are optimized by default

Description

This function creates a list of parameters used in the xcms-methods retcor.obiwarp and group.density. Per default the following parameters have a defined range where optimization should start:
retcor.obiwarp parameters: 'gapInit'; 'gapExtend', 'profStep'
group.density parameters: 'bw', 'minfrac', 'mzwid'

Usage

  getDefaultRetGroupStartingParams(retcorMethod=c("obiwarp", "loess", "none"), 
  distfunc=c("cor_opt", "cor", "cov", "prd", "euc"), high_resolution=TRUE)

Arguments

retcorMethod	The name of the retention time correction method that should be used. The XCMS methods retcor.obiwarp and retcor.loess are supported. If no retention time correction should be done use "none".
distfunc	The name of the distance function used by retcor.obiwarp
high_resolution	If high_resolution = TRUE starting values for mzwid are set to 0.015 and 0.035; if high_resolution = FALSE to 0.15, 0.35

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$max <- c(4,8))
* If you dont want to optimize a parameter set a default value (e.g. params$max <- 10)

Value

A List of parameters used in the xcms-methods retcor.obiwarp or retcor.loess and group.density

Author(s)

Gunnar Libiseller

Examples

params <- getDefaultRetGroupStartingParams()
params$bw <- 10
params$max <- c(4,8)
params

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