peakpicking_optimization: Peak picking optimization

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

Description

The function optimize parameters considering a set of samples for the peak picking algorithm using the IPO Package. This includes Peak Detection (‘Centwave), Retention Time Correction (‘obiwarp’) and Peak Correspondence (‘Density’).

Usage

peakpicking_optimization(
  dataset,
  peakpickingParameters,
  nSlaves = 1,
  opt_path,
  subdir = "plot_ipo",
  plots = TRUE,
  format = "mzXML"
)

Arguments

dataset	A lcms_dataset
peakpickingParameters	Parameters for peak picking
nSlaves	Number of slaves the optimization process should spawn.
opt_path	Path where optimization samples are saved.
subdir	Folder where surface plots are saved. 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 peak picking list with the best setting.

See Also

Other dataset functions: IPO_group_peaks(), find_peaks_cwp(), lcms_dataset_load(), lcms_dataset_save(), lcms_fill_chrom_peaks(), lcms_filter_mz(), lcms_filter_polarity(), lcms_filter_rt_min(), lcms_filter_sample_type(), lcms_meta_add(), lcms_meta_export(), lcms_plot_chrom_peak_image(), lcms_plot_tics(), lcms_rearrange_datafiles_by_class(), lcms_retention_time_alignment_plot(), lcms_tics(), obiAdjust_Rtime(), phData()

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

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

Examples

## Not run: 
opt_path <- system.file("extdata", "ipo_opt", package = "AlpsLCMS")
file_name <- system.file("extdata", "dataset_pos_rt_rs.rds", package = "AlpsLCMS")
dataset <- lcms_dataset_load(file_name)
default_peakpicking_params <- default_peakpicking_params(optimize = TRUE)
result_peakpicking <- peakpicking_optimization(dataset,
                                                   default_peakpicking_params,
                                                   opt_path = opt_path,
                                                   subdir = NULL)

## End(Not run)

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