IPO_group_peaks: Peak Correspondence

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

Description

Peak correspondence is carried out by the 'lcms_groupChromPeaks' method, with parameters obtained form IPO. Peak Correspondece consist in grouping peaks on retention time axis with the purspose of associate them to spectra on the mass/chage axis.

Usage

IPO_group_peaks(peakdet_align, params)

Arguments

peakdet_align	A lcms_dataset with (1) detected (findChromPeaks_cwp function) and (2) aligned (obiAdjust_Rtime function) peaks.
params	A converted parameters template from IPO parameters.

Details

Note: signal processing generally consists in three main steps: (1) peak detection (find_peaks_cwp function), (2) peak alignment (obiAdjust_Rtime function) and (3) peak correspondence (IPO_group_peaks function). The optimized set of parameters for this signal preprocessing can be obatained from IPO Package.

After this stage the peak table is finally obtained.

Value

A lcms_dataset with (1) detected (find_peaks_cwp function), (2) aligned (align_rtime function) and (3) grouped (IPO_group_peaks function) peaks.

See Also

Other dataset functions: find_peaks_cwp(), lcms_dataset_load(), lcms_dataset_save(), lcms_fill_chrom_peaks(), lcms_filter_mz(), lcms_filter_polarity(), lcms_filter_rt_min(), lcms_filter_sample_type(), lcms_meta_add(), lcms_meta_export(), lcms_plot_chrom_peak_image(), lcms_plot_tics(), lcms_rearrange_datafiles_by_class(), lcms_retention_time_alignment_plot(), lcms_tics(), obiAdjust_Rtime(), peakpicking_optimization(), phData()

Examples

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


peak_table <- IPO_group_peaks(peakdet_align, params = preproc_params)
print(peak_table)

## End(Not run)

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