R: Set the "normalized" and "normalization" attributes

setNormalized {photobiology}

R Documentation

Set the "normalized" and "normalization" attributes

Description

Function to write the "normalized" attribute of an existing generic_spct object.

Usage

setNormalized(
  x,
  norm = FALSE,
  norm.type = NA_character_,
  norm.factors = NA_real_,
  norm.cols = NA_character_,
  norm.range = rep(NA_real_, 2),
  verbose = getOption("verbose_as_default", default = FALSE)
)

setNormalised(
  x,
  norm = FALSE,
  norm.type = NA_character_,
  norm.factors = NA_real_,
  norm.cols = NA_character_,
  norm.range = rep(NA_real_, 2),
  verbose = getOption("verbose_as_default", default = FALSE)
)

Arguments

`x`	a generic_spct object.
`norm`	numeric (or logical) Normalization wavelength (nanometres).
`norm.type`	character Type of normalization applied.
`norm.factors`	numeric The scaling factor(s) so that dividing the spectral values by this factor reverts the normalization.
`norm.cols`	character The name(s) of the data columns normalized.
`norm.range`	numeric The wavelength range used for normalization (nm).
`verbose`	logical Flag enabling or silencing informative warnings.

Details

This function is used internally, although occasionally users may want to use it to "pretend" that spectral data have not been normalized. Use normalize() methods to apply a normalization and set the attributes accordingly. Function setNormalized() only sets the attributes that store the metadata corresponding to an already applied normalization. Thus a trace of the transformations applied to spectral data is kept, which currently is used to renormalize the spectra when the quantity used for expression is changed with a conversion function. It is also used in other packages like 'ggspectra' when generating automatically axis labels. If x is not a generic_spct object, x is not modified.

Note

Passing a logical as argument to norm is deprecated but accepted silently for backwards compatibility.