lcms_to_mait: Convert xcms to MAIT

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

Description

Function to create a MAIT object using data from xcms.

Usage

lcms_to_mait(
  data_dir = NULL,
  project_dir = NULL,
  project = NULL,
  preproc_params = NULL,
  peak_table = NULL
)

Arguments

data_dir	directory with LC-MS datafiles.
project_dir	path to the the project directory.
project	name of the.
preproc_params	params from XCMS.
peak_table	XCMS procesed LC-MS data.

Details

MAIT Package allows to annotate the peaks of the peak table provided by XCMS. *Note: The dataset must be converted from an object of the XCMS Package to an object of the MAIT Package.

Value

A MAIT object.

See Also

Other metabolite identification functions: lcms_identify_metabolites(), lcms_peak_annotation(), lcms_peak_table_boxplots(), lcms_peak_table_pca(), lcms_raw_data(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_write_parameter_table()

Other dataset_peak_table functions: lcms_dataset_load(), lcms_identify_metabolites(), lcms_peak_annotation(), lcms_peak_table_boxplots(), lcms_peak_table_pca(), lcms_plot_tics(), lcms_raw_data(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_tics()

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_write_opt_params(), lcms_write_parameter_table(), phData()

Examples

## Not run: 
file_name <-  system.file("extdata", "peak_table_imputed.rds", package = "AlpsLCMS")
peak_table <- base::readRDS(file_name)
opt_result_path <-  system.file("extdata", package = "AlpsLCMS")
preproc_params <- lcms_read_ipo_to_xcms(opt_result_path)

data_dir <-  system.file("extdata", "rearrange_mait", package = "AlpsLCMS")
project_dir <-  system.file("extdata", package = "AlpsLCMS")
project <- "project"

peak_table_mait <- lcms_to_mait(data_dir = data_dir,
                                project_dir = project_dir,
                                project = project,
                                preproc_params = preproc_params,
                                peak_table = peak_table)
print(peak_table_mait)

## End(Not run)

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.