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Find Local Extrema in NMR Spectra (Peak Picking)

Source: R/ppick.R
ppick.Rd

Identifies local maxima, minima, or both from smoothed NMR spectra using Savitzky–Golay filtering.

Usage

ppick(X, ppm, fil_p = 3, fil_n = 5, type = "max")

Arguments

X

Numeric matrix. NMR data with spectra in rows and chemical shifts in columns.

ppm

Numeric vector. Chemical shift values corresponding to columns in X.

fil_p

Integer. Polynomial order of the Savitzky–Golay filter.

fil_n

Integer. Filter length (must be odd) of the Savitzky–Golay filter.

type

Character. Type of extrema to return: "max", "min", or "both".

Value

A list of data frames, one per spectrum. Each data frame contains:

  • idc: Index of the detected peak.

  • ppm: Chemical shift at the peak.

  • Int: Intensity at the peak.

  • Etype: Extrema type: 1 for minima, -1 for maxima.

Details

The spectra are smoothed using a Savitzky–Golay filter to reduce noise. Extrema are then detected by identifying sign changes in the first derivative of the smoothed signal.

See also

sgolayfilt

Examples

data(covid)
X <- covid$X
ppm <- covid$ppm

peaks <- ppick(X, ppm)
spec(X[1, ], ppm, shift = c(4.2, 5.3))


points(peaks[[1]]$ppm, peaks[[1]]$Int, col = factor(peaks[[1]]$Etype))
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet