find_peaks_cwp: Chromatographic peak detection (CentWave)
In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description Usage Arguments Details Value See Also Examples

The findChromPeaks_cwp function performs the chromatographic peak detection on LC/GC-MS data. The standard method for peak detection is 'CentWave'. Peak detection aims to detect important features (peaks) on the chromatographic axis. This will be useful for a posterior peak alignment on the chormatophic axis.

1	find_peaks_cwp(dataset, params)

`dataset`	A lcms_dataset.
`params`	A converted parameters template from IPO parameters.

Note: signal processing generally consists in three main steps: (1) peak detection (lcms_find_chromp_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.

A lcms_dataset with the detected peaks added.

Other dataset functions: IPO_group_peaks(), 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()

## Not run: 
file_path <- system.file("extdata", "rearrange_mait", package = "AlpsLCMS")
samples_mzxml <- list.files(file_path, recursive = TRUE, full.names = TRUE)
meta_path <- system.file("extdata", "metadata.xlsx", package = "AlpsLCMS")
opt_result_path <-  system.file("extdata", package = "AlpsLCMS")
preproc_params <- lcms_read_ipo_to_xcms(opt_result_path)

dataset <- suppressWarnings(lcms_read_samples(samples_mzxml, mode = "onDisk"))
metadata <- lcms_meta_read(meta_path)
dataset_meta <- lcms_meta_add(dataset, metadata, by = "sampleNames")

peakdet <- find_peaks_cwp(dataset_meta, params = preproc_params)
print(peakdet)

## End(Not run)