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Full Width at Half Maximum (FWHM) Estimation

Source: R/utils_nmr_qc.R
lw.Rd

Estimates the full width at half maximum (FWHM; line width) of a singlet-like peak within a specified chemical-shift range for each spectrum.

Usage

lw(X, ppm = NULL, shift = c(-0.1, 0.1), sf)

Arguments

X

Numeric matrix (spectra in rows) or a named list as returned by read1d/read1d_proc containing X, ppm, and meta.

ppm

Numeric vector of chemical shift values (ppm) corresponding to columns of X. If NULL, ppm is inferred in the following order:

  1. attr(X, "m8_axis")$ppm (if present),

  2. numeric colnames(X) (if present).

shift

Numeric vector of length 2. Chemical shift range containing the peak (e.g., c(-0.1, 0.1) for TSP).

sf

Spectrometer frequency in MHz. Either a single numeric (recycled across spectra) or a numeric vector of length nrow(X) (one value per spectrum). If X is a list input and sf is missing, sf is taken from X$meta$a_SFO1 when available. If sf is missing for a matrix input, the function attempts to use attr(X, "m8_meta")$a_SFO1 when present.

Value

Numeric vector of FWHM values in Hz (length nrow(X)).

Details

For each spectrum, the function:

  1. extracts the region defined by shift,

  2. finds the peak apex within that region,

  3. computes the half-height level relative to the local baseline (minimum in the window),

  4. estimates the left and right half-height crossing points by linear interpolation,

  5. converts the width from ppm to Hz using sf (MHz), i.e. Hz = ppm * sf.

If no valid half-height crossings can be found (e.g., very low SNR or truncated peak), NA is returned for that spectrum.

Note

The ppm axis may be increasing or decreasing; FWHM is computed as an absolute width and is therefore independent of axis direction.

Examples

# Simulated NMR peaks with different linewidths
ppm <- seq(-0.2, 0.2, length.out = 1000)

# generate peaks with increasing width
sds <- seq(0.01, 0.03, length.out = 10)

X <- t(sapply(sds, function(s)
  dnorm(ppm, mean = 0, sd = s)
))

sf <- 600  # spectrometer frequency in MHz

fwhm_vals <- lw(X, ppm = ppm, shift = c(-0.1, 0.1), sf = sf)

plot(sds, fwhm_vals,
  xlab = "Gaussian sd",
  ylab = "Estimated FWHM (Hz)",
  pch = 16)