lcms_sig_peaks_table: Significant feature information

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

Description

Function lcms_sig_peaks_table takes an MAIT-class object containing significant feature information and builds a table with the information related to these features.

Usage

lcms_sig_peaks_table(
  MAIT.object = NULL,
  printCSVfile = FALSE,
  extendedTable = TRUE,
  printAnnotation = TRUE
)

Value

A table containing: First column (mz): Peak mass Second column (mzmin): Minimum peak mass of the peak group. Third column (mzmax): Maximum peak mass of the peak group. Fourth column (rt): Peak retention time (in minutes). Fifth column (rtmin): Minimum peak retention time of the peak group. Sixth column (rtmax): Maximum peak retention time of the peak group. Seventh column (npeaks): Number of samples where the peak has been detected. The columns from the nineth to the column labeled "isotopes" contain number of class samples where the peak has been detected and the intensities of the peak among samples.

The isotopes column shows if the peak has been identified as a possible isotope.

The adduct column shows which kind of adduct could the peak be.

The column labeled pcgroup contains the spectral ID of the peak.

The P.adjust column contains the corrected peak p-value using post-hoc methods. The p column shows the peak p-value with no multiple test correction.

The Fisher column shows the Fisher test results for the peak. Each of the letters separated by the character "_" corresponds to a class value. Classes having the same letters are indistinguible whereas those having different letters are statistically different clases.

The last columns contain the mean and median values for each feature.

See Also

Other metabolite identification functions: lcms_identify_metabolites(), lcms_peak_annotation(), lcms_peak_table_boxplots(), lcms_peak_table_pca(), lcms_raw_data(), lcms_spectral_sig_features(), lcms_to_mait(), 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_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_peak_annotation(), lcms_raw_data(), lcms_read_ipo_to_xcms(), lcms_read_samples(), lcms_rearrange_datafiles_by_class(), 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 <- base::readRDS(file_name)
sig_table <- lcms_sig_peaks_table(peak_table,  printCSVfile=FALSE)
str(sig_table)

## End(Not run)

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