lcms_retcorgroup_optimization: Optimization of retention time correction and grouping...

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

Description

The function optimizes parameters considering a set of samples for the retention time correction and grouping using the IPO Package.

Usage

lcms_retcorgroup_optimization(
  optimizedXcmsSetObject,
  retcorGroupParameters,
  nSlaves = 1,
  opt_path,
  subdir = "plot_ipo",
  plots = TRUE
)

Arguments

optimizedXcmsSetObject	XCMS object conatining the best_settings parameters. This object may be created after running peakpicking_optimization and extract best_settings$xset (e.g. optimizedXcmsSetObject <- resultPeakpicking$best_settings$xset)
retcorGroupParameters	Parameters for retention time correction and optimization
nSlaves	Number of slaves the optimization process should spawn.
opt_path	Path where optimization samples are saved.
subdir	Folder where surface plots are save. If NULL they are displayed by the graphical device.
plots	Defines if plots should be generated (TRUE) or not (FALSE) in a subfolder called "plot_ipo"(default).

Value

A list with the optimization of parameters for retention time and grouping.

See Also

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

Other visualization functions: lcms_peak_table_boxplots(), lcms_peak_table_pca(), lcms_plot_chrom_peak_image(), lcms_plot_chrom(), lcms_plot_tics(), lcms_retention_time_alignment_plot(), peakpicking_optimization()

Examples

## Not run: 
file_name_pp <- system.file("extdata", "result_peakpicking.rds", package = "AlpsLCMS")
optimizedXcmsSetObject <-base::readRDS(file_name_pp)$best_settings$xset
file_name_rcg <- system.file("extdata", "default_retcorgroup_params.rds", package = "AlpsLCMS")
default_retcorgroup_params <- base::readRDS(file_name_rcg)
opt_path <-  system.file("extdata", package = "AlpsLCMS")

result_retcorgroup <- lcms_retcorgroup_optimization(optimizedXcmsSetObject,
                                                   default_retcorgroup_params,
                                                   opt_path = opt_path,
                                                   subdir = NULL)

## End(Not run)

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