lcms_peak_annotation: Peak Annotation

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

Description

The AlpsLCMS Package allows to annotate the peaks of the peak table provided by XCMS. This is done in two different stages:

• Annotation with CAMERA.

• Annotation using predefined biotransformation.

Usage

lcms_peak_annotation(
  MAIT.object = NULL,
  corrWithSamp = 0.7,
  perfwhm = 0.6,
  sigma = 6,
  adductTable = NULL,
  printSpectraTable = TRUE,
  corrBetSamp = 0.75,
  pval = 0.05,
  calcIso = TRUE,
  calcCiS = TRUE,
  calcCaS = TRUE,
  graphMethod = "hcs",
  annotateAdducts = TRUE
)

Details

*Note: The dataset must be converted from an object of the XCMS Package to an object of the MAIT Package.

Value

A MAIT-class object with xsAnnotate-class in the rawData slot.

See Also

Other metabolite identification functions: lcms_identify_metabolites(), 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_identify_metabolites(), 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_identify_metabolites(), lcms_meta_export(), lcms_meta_read(), 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_mait.rds", package = "AlpsLCMS")
peak_table <- base::readRDS(file_name)
peak_table_ann <- lcms_peak_annotation(MAIT.object = peak_table)
lcms_raw_data(peak_table_ann)

## End(Not run)

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