lcms_write_opt_params: Displaying and Storing optimized settings

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

Description

The function allows visulizing the parameter optimization results by IPO Package allows in the RStudio console. Also you can save this results in plain text files (i.e. a .CVS file).

Usage

lcms_write_opt_params(
  results_pp,
  results_rtcg,
  opt_result_path,
  csv = TRUE,
  console = TRUE
)

Arguments

results_pp	object from the peakpicking_optimization function. If NULL, the default parameters for xcms are loaded.
results_rtcg	object from the lcms_corgroup_optimization function.
opt_result_path	A directory to save the parameters file.
csv	if TRUE, it writes a file in csv format.
console	if TRUE, it displays the params on the console.

Value

A file with the params from the IPO optimization.

See Also

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

Other import/export functions: lcms_convert_ipo_to_xcms(), lcms_dataset_load(), lcms_dataset_save(), lcms_identify_metabolites(), lcms_meta_export(), lcms_meta_read(), lcms_peak_annotation(), lcms_raw_data(), lcms_read_ipo_to_xcms(), lcms_read_samples(), lcms_rearrange_datafiles_by_class(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_to_mait(), lcms_write_parameter_table(), phData()

Examples

## Not run: 
 opt_result_path <-system.file("extdata", "ipo_opt", package = "AlpsLCMS")
 file_name_pp <- system.file("extdata", "result_peakpicking.rds", package = "AlpsLCMS")
 file_name_rcg <- system.file("extdata", "result_retcorgroup.rds", package = "AlpsLCMS")
 result_peakpicking <- base::readRDS(file_name_pp)
 result_retcorgroup <- base::readRDS(file_name_rcg)

 lcms_write_opt_params(result_peakpicking, result_retcorgroup, opt_result_path)
 
## End(Not run)

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