files_to_rDolphin: Files to rDoplhin

In AlpsNMR: Automated spectraL Processing System for NMR

Description

The rDolphin family functions are introduced to perform automatic targeted metabolite profiling. Therefore, ensure that you interpolated from -0.1 ppm in order to consider the TSP/DSS signal at 0.0 ppm. The function generates a list with the files required by to_rDolphin function. Then, it is required to save them with the save_files_to_rDolphin. to_rDolphin function will read the generated "parameters.csv" file. function.

Usage

files_to_rDolphin(nmr_dataset, biological_origin)

Arguments

nmr_dataset	An nmr_dataset object
biological_origin	String specify the type of sample (blood, urine, cell)

Value

a list containing:

• meta_rDolphin: metadata in rDolphin format,

• NMR_spectra: spectra matrix

• ROI: ROI template

• Parameters: parameters file

See Also

Other import/export functions: Pipelines, load_and_save_functions, nmr_data(), nmr_meta_export(), nmr_read_bruker_fid(), nmr_read_samples(), nmr_zip_bruker_samples(), save_files_to_rDolphin(), save_profiling_output(), to_ChemoSpec()

Other nmr_dataset_1D functions: [.nmr_dataset_1D(), computes_peak_width_ppm(), file_lister(), format.nmr_dataset_1D(), is.nmr_dataset_1D(), load_and_save_functions, new_nmr_dataset_1D(), nmr_align_find_ref(), nmr_baseline_removal(), nmr_baseline_threshold(), nmr_exclude_region(), nmr_integrate_regions(), nmr_interpolate_1D(), nmr_meta_add(), nmr_meta_export(), nmr_meta_get_column(), nmr_meta_get(), nmr_normalize(), nmr_pca_build_model(), nmr_pca_outliers_filter(), nmr_pca_outliers_plot(), nmr_pca_outliers_robust(), nmr_pca_outliers(), nmr_ppm_resolution(), plot.nmr_dataset_1D(), plot_webgl(), print.nmr_dataset_1D(), rdCV_PLS_RF_ML(), rdCV_PLS_RF(), save_files_to_rDolphin(), to_ChemoSpec(), validate_nmr_dataset_peak_table(), validate_nmr_dataset()

Examples

## Not run: 
# Set the directory in which rDolphin files will be saved
output_dir_10_rDolphin <- file.path(your_path, "10-rDolphin")
fs::dir_create(output_dir_10_rDolphin)

# Generate the files (for plasma/serum)
files_rDolphin = files_to_rDolphin(nmr_dataset_0_10_ppm, blood)

# Save the files
save_files_to_rDolphin(files_rDolphin, output_dir_10_rDolphin)

# Build the rDolphin object. Do not forget to set the directory
setwd(output_dir_10_rDolphin)
rDolphin_object = to_rDolphin("Parameters.csv")

# Visualize your spectra
rDolphin_plot(rDolphin_object)

# Run the main profiling function (it takes a while)
targeted_profiling = Automatic_targeted_profiling(rDolphin_object)

# Save results
save_profiling_output(targeted_profiling, output_dir_10_rDolphin)

save_profiling_plots(output_dir_10_rDolphin, targeted_profiling$final_output,
targeted_profiling$reproducibility_data)

#Additionally, you can run some stats
intensities = targeted_profiling$final_output$intensity
group = as.factor(rDolphin_object$Metadata$type)
model_PLS <- rdCV_PLS_RF(X = intensities, Y = group)

## End(Not run)

AlpsNMR documentation built on April 1, 2021, 6:02 p.m.