lcms_rearrange_datafiles_by_class: Rearrange datafiles by class
In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description Usage Arguments Value See Also Examples

Although Data Preprocessing can be performed using any filepath with the xcms Package, it is convenient to rearrange data files by sample class (that is, all the samples belonging to the same sample class are included in the same folder). This is done because, after the preprocessing stage, MAIT Package takes care of Data Annotation and Metabolite Identification. MAIT needs a specific directory structure for data managing. Otherwise, it can't work properly.

1	lcms_rearrange_datafiles_by_class(dataset, dataDir)

`dataset`	A lcms_dataset.
`dataDir`	A directory in where LC-MS files are going to be saved.

LC-MS datafiles sorted by class treatment.

Other dataset functions: IPO_group_peaks(), 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_retention_time_alignment_plot(), lcms_tics(), obiAdjust_Rtime(), peakpicking_optimization(), phData()

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_sig_peaks_table(), lcms_spectral_sig_features(), lcms_to_mait(), lcms_write_opt_params(), lcms_write_parameter_table(), phData()

## Not run: 
file_name <- system.file("extdata", "dataset_pos_rt_rs.rds", package = "AlpsLCMS")
dataset <- lcms_dataset_load(file_name)
path <- system.file("extdata","rearrange_mait", package = "AlpsLCMS")
lcms_rearrange_datafiles_by_class(dataset = dataset,
                            dataDir = path)
fileList = list.files(path = paste(path, list.files(path = path),
                           sep = "/"), full.names = TRUE)
print(fileList)

## End(Not run)