feemscale {albatross}

Rescale FEEM spectra to a given norm and remember the scale factor

Description

Given a norm function (typically, standard deviation), scale the intensities in FEEM objects to it and optionally remember the scale factor.

Usage

  feemscale(x, ...)
  ## S3 method for class 'feem'
feemscale(x, norm = sd, remember = TRUE, ...)
  ## S3 method for class 'feemcube'
feemscale(x, ..., progress = FALSE)
  ## S3 method for class 'list'
feemscale(x, ..., progress = FALSE)

Arguments

x

A FEEM object, a FEEM cube object, or a list of anything compatible with feemscale generic.

norm

A function taking a numeric matrix and returning its norm. Typically, sd or sumsq.

remember

Whether to remember the scale factor. If FALSE, the scale factor in the returned object is unchanged.

...

Passed as-is to feemscale, to feemscale.feem, then to the norm function. Use this to set na.rm = TRUE for functions like sd or sumsq.

progress

Set to TRUE to enable a progress bar (implemented via txtProgressBar).

Value

feemscale.feem: a FEEM object with intensities divided by scale factor (norm(x)) and its scale attribute multiplied by the scale factor.

feemscale.feemcube: a FEEM cube built from FEEM objects scaled as described above.

feemscale.list: a list consisting of results of feemscale generic applied to its elements.

References

Bro R, Smilde AK (2003). “Centering and scaling in component analysis.” Journal of Chemometrics, 17(1), 16-33. doi:10.1002/cem.773.

See Also

feem

Examples

  feemscale(feem(matrix(1:42, 6), 1:6, 1:7))