ChemoSpecUtils: removeFreq – R documentation

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removeFreq

Remove Frequencies from a Spectra or Spectra2D Object

Description

This function removes specified frequencies from a Spectra or Spectra2D object. For instance, one might want to remove regions lacking any useful information (to reduce the data size), remove regions with large interfering peaks (e.g. the water peak in 1H NMR) or simply focus on a region of interest.

Usage

removeFreq(spectra, rem.freq = NULL, remF2 = NULL, remF1 = NULL)

Arguments

`spectra`	An object of S3 class `Spectra` or `Spectra2D` from which to remove frequencies.
`rem.freq`	For a `Spectra` object, a vector of logicals. `rem.freq` can be any valid `R` statement that leads to a vector of logicals (must be of `length(Spectra$freq)`). This vector should be `TRUE` for frequencies you want to be removed and `FALSE` for those frequencies which will be kept. In the examples, the \| and & operators may seem backward in a sense, but R evaluates them one at a time and then combines them to give the desired result. You may wish to look at `Comparison` and `Logic`. See the examples. In addition, since January 2020 `rem.freq` may be a formula as described below.
`remF2`	Applies to `Spectra2D` objects. A formula giving the range of frequencies to be extracted. May include "low" or "high" representing the extremes of the spectra. Values outside the range of F2 are tolerated without notice and are handled as `min` or `max`. See the examples.
`remF1`	As for `remF2`.

Value

An object of S3 class Spectra or Spectra2D.

Modifying Spectra2D Objects

Regarding Spectra2D objects, one cannot remove frequencies from the interior of a 2D NMR data set and expect to get a meaningful contour plot, because doing so puts unrelated peaks adjacent in the data set. This would lead to contours being drawn that don't exist in the original data set. However, one can remove data from the interior and run a PARAFAC analysis on the result, using the spectrum as an abstract object (that is, the spectrum may not plottable, but the resulting scores are still meaningful).

Author(s)

Bryan A. Hanson, DePauw University.

Examples

if (checkForPackageWithVersion("ChemoSpec", "5.1")) {
  library("ChemoSpec")
  data(SrE.IR)
  sumSpectra(SrE.IR)

  # Examples where rem.freq is a logical vector

  # Remove frequencies from one end:
  newIR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 3500)

  # Remove frequencies from both ends at once:
  newIR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 3500
  | SrE.IR$freq < 800)

  # Remove frequencies from the middle:
  newIR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 800
  & SrE.IR$freq < 1000)

  # The logic of this last one is as follows.  Any values
  # that are TRUE will be removed.
  values <- 1:7
  values > 2
  values < 6
  values > 2 & values < 6

  # Examples where rem.freq is a formula

  # Remove frequencies from one end:
  newIR <- removeFreq(SrE.IR, rem.freq = 3500 ~ high)

  # Remove frequencies from both ends is a two step process with formulas:
  newIR <- removeFreq(SrE.IR, rem.freq = 3500 ~ high)
  newIR <- removeFreq(newIR, rem.freq = low ~ 800)

  # Remove frequencies from the middle:
  newIR <- removeFreq(SrE.IR, rem.freq = 800 ~ 1000)

  # After any of these, inspect the results:
  sumSpectra(newIR)
}

if (checkForPackageWithVersion("ChemoSpec2D", "0.3")) {
  library("ChemoSpec2D")
  data(MUD1)

  plotSpectra2D(MUD1,
    which = 7, lvls = seq(-1, 1, by = 0.2),
    main = "MUD1 Sample 7: Complete Data Set"
  )

  MUD1a <- removeFreq(MUD1, remF2 = 2 ~ 4)
  sumSpectra(MUD1a) # cannot plot, results would be misleading

  MUD1b <- removeFreq(MUD1, remF1 = low ~ 20)
  sumSpectra(MUD1b)
  plotSpectra2D(MUD1b,
    which = 7, lvls = seq(-1, 1, by = 0.2),
    main = "MUD1 Sample 7\nRemoved Frequencies: F1 low ~ 20"
  )

  MUD1c <- removeFreq(MUD1, remF2 = low ~ 2)
  sumSpectra(MUD1c)
  plotSpectra2D(MUD1c, ,
    which = 7, lvls = seq(-1, 1, by = 0.2),
    main = "MUD1 Sample 7\nRemoved Frequencies: F2 low ~ 2"
  )

  MUD1d <- removeFreq(MUD1, remF2 = 3 ~ high, remF1 = 45 ~ 55)
  sumSpectra(MUD1d) # not plotted, results would be misleading
}

ChemoSpecUtils

Functions Supporting Packages ChemoSpec and ChemoSpec2D

v0.4.96

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)

Initial release

2021-03-15