lcms_identify_metabolites: Metabolite search

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

Description

Takes a MAIT object and performs the metabolite search for the significant features

Usage

lcms_identify_metabolites(
  MAIT.object = NULL,
  peakTolerance = 0.005,
  database = NULL,
  polarity = "positive",
  printCSVfile = TRUE
)

Value

An output table is stored in the folder (working directory)/tables/SearchTable.csv if printCSVfile is set to TRUE. More info at metaboliteTable.

See Also

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

Other dataset_peak_table functions: lcms_dataset_load(), 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(), lcms_to_mait()

Other import/export functions: lcms_convert_ipo_to_xcms(), lcms_dataset_load(), lcms_dataset_save(), 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_opt_params(), lcms_write_parameter_table(), phData()

Examples

## Not run: 
file_name <- system.file("extdata", "peak_table_sig_ann.rds", package = "AlpsLCMS")
peak_table <- readRDS(file_name)
metabololite_table <- lcms_identify_metabolites(MAIT.object = peak_table,
                              peakTolerance = 0.005)

## End(Not run)

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