lcms_default_retcorgroup_params: Default parameters for optimization of retention time...

In sipss/NIHSlcms: Signal processing of LC-MS metabolomics

Description

The function creates default parameters for optimizing retention time correction and grouping algorithms. Parameter optimization on the XCMS preprocessing algorithms is performed using the IPO Package. Use this function to create the template within lcms_corgroup_optimization function.

Usage

lcms_default_retcorgroup_params(
  profStep = c(0.7, 1),
  gapExtend = c(2.1, 2.7),
  optimize = TRUE
)

Arguments

profStep	set the m/z step for generating profile (matrix) data from raw mass spectral data. Smaller steps yield more precision at the cost of greater memory usage.
gapExtend	numeric(1) defining the penalty for gap enlargement. The default value for gapExtend depends on the value of distFun, for distFun = "cor" and distFun = "cor_opt" it is 2.4, for distFun = "cov" 11.7, for distFun = "euc" 1.8 and for distFun = "prd" 7.8.
optimize	by default is TRUE. If FALSE, the function does not optimize the parameters.

Value

A parameters template for retention time correction and grouping optimization

Examples

## Not run: 
default_retcorgroup_params <- lcms_default_retcorgroup_params(optimize = TRUE)
print(default_retcorgroup_params)

## End(Not run)

sipss/NIHSlcms documentation built on May 13, 2021, 6:19 p.m.