default_peakpicking_params: Default parameters for peak picking optimization

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

Description

The function creates default parameters for optimizing peakpicking algorithms.Parameter optimization on the XCMS preprocessing algorithms was performed using the IPO Package. This includes Peak Detection (‘Centwave’), Retention Time Correction (‘obiwarp’) and Peak Correspondence (‘Density’). Use this function to generate the template within the peakpicking_optimization function.

Usage

default_peakpicking_params(
  noise = c(1e+05, 1e+07),
  snthresh = c(3, 5),
  min_peakwidth = c(9, 20),
  max_peakwidth = c(35, 50),
  optimize = TRUE
)

Arguments

noise	numeric, minimum intensity needed to be included in the analysis.
snthresh	numeric, set the signal to noise ratio threshold to be included.
min_peakwidth	numeric (two values) with the expected minimal peak width in chromatographic dimension. Set as a range (min, max) in seconds.
max_peakwidth	numeric (two values) with the expected maximum peak width in chromatographic dimension. Set as a range (min, max) in seconds.
optimize	by default is TRUE. If FALSE, the function does not initialze the parameters the parameters

Value

A parameters template for peak picking optimization

See Also

Other optimization functions: lcms_convert_ipo_to_xcms(), lcms_read_ipo_to_xcms(), lcms_retcorgroup_optimization(), lcms_write_opt_params(), peakpicking_optimization()

Examples

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

## End(Not run)

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