nmr_normalize: Normalize nmr_dataset_1D samples

In AlpsNMR: Automated spectraL Processing System for NMR

Description

The nmr_normalize function is used to normalize all the samples according to a given criteria.

Usage

nmr_normalize(
  samples,
  method = c("area", "max", "value", "region", "pqn", "none"),
  ...
)

nmr_normalize_extra_info(samples)

Arguments

samples	A nmr_dataset_1D object
method	The criteria to be used for normalization - area: Normalize to the total area - max: Normalize to the maximum intensity - value: Normalize each sample to a user defined value - region: Integrate a region and normalize each sample to that region - pqn: Use Probabalistic Quotient Normalization for normalization - none: Do not normalize at all
...	Method dependent arguments: - method == "value": - value: A numeric vector with the normalization values to use - method == "region": - ppm_range: A chemical shift region to integrate - ...: Other arguments passed on to nmr_integrate_regions

Details

The nmr_normalize_extra_info function is used to extract additional information after the normalization. Typically, we want to know what was the actual normalization factor applied to each sample. The extra information includes a plot, representing the dispersion of the normalization factor for each sample.

Value

The nmr_dataset_1D object, with the samples normalized. Further information for diagnostic of the normalization process is also saved and can be extracted by calling nmr_normalize_extra_info() afterwards.

See Also

Other nmr_dataset_1D functions: [.nmr_dataset_1D(), computes_peak_width_ppm(), file_lister(), files_to_rDolphin(), 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_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

nmr_dataset <- nmr_dataset_load(system.file("extdata", "nmr_dataset.rds", package = "AlpsNMR"))
nmr_dataset <- nmr_normalize(nmr_dataset, method = "area")
norm_dataset <- nmr_normalize(nmr_dataset)
norm_dataset$plot
nmr_dataset <- nmr_dataset_load(system.file("extdata", "nmr_dataset.rds", package = "AlpsNMR"))
nmr_dataset <- nmr_normalize(nmr_dataset, method = "area")
norm_extra_info <- nmr_normalize_extra_info(nmr_dataset)
norm_extra_info$plot

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