nmr_normalize: Normalize nmr_dataset_1D samples

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

Normalize nmr_dataset_1D samples

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 aim is to correct from changes between samples, so no matter the criteria used to normalize, once we get the factors (e.g. the areas), we divide them by the median normalization factor to avoid introducing global scaling factors.

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 basic functions: nmr_exclude_region()

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

sipss/AlpsNMR documentation built on Aug. 13, 2024, 5:11 p.m.