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Peak picking using Savitzky–Golay derivatives

Source: R/features_ppick.R
ppick2.Rd

Finds local extrema in 1D spectra using Savitzky–Golay first and second derivatives. Candidate peaks are identified at zero-crossings of the first derivative and classified by the sign of the second derivative. Optional filters control peak height, prominence, SNR, curvature and minimum separation.

Usage

ppick2(
  X,
  ppm = NULL,
  type = c("max", "min", "both"),
  fil_p = 3L,
  fil_n = 11L,
  noise_win = NULL,
  min_snr = 10,
  min_height = NULL,
  min_prominence = NULL,
  prom_half_window_ppm = 0.02,
  min_distance_ppm = 0.005,
  min_curvature = NULL,
  keep_cols = c("height", "snr", "curvature", "prominence")
)

Arguments

X

Numeric matrix or vector. Spectra in rows.

ppm

Numeric vector or NULL. If NULL, inferred from colnames(X).

type

Character. "max", "min", or "both".

fil_p

Integer. Polynomial order for SG filter.

fil_n

Integer. Window length for SG filter (odd).

noise_win

Numeric length-2 vector or NULL. Ppm window used to estimate noise per spectrum. If NULL, a robust noise estimate is computed from the full spectrum (MAD of first differences).

min_snr

Numeric. Minimum SNR (peak height / noise). Set NULL to disable.

min_height

Numeric. Minimum absolute peak height (in original intensity units). NULL disables.

min_prominence

Numeric. Minimum local prominence. NULL disables.

prom_half_window_ppm

Numeric. Half-window (ppm) for prominence estimation around each peak.

min_distance_ppm

Numeric. Minimum separation between peaks (ppm). NULL disables.

min_curvature

Numeric. Minimum absolute curvature at peak (|d2|). NULL disables.

keep_cols

Character. Extra columns to keep (default keeps all computed).

Value

List of data.frames (one per spectrum). Each contains: idc, ppm, Int, Etype (+1 max, -1 min), height, snr, curvature, prominence.

Examples

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

peaklist <- ppick2(X[1,], ppm, min_snr=50)

plot_spec(X[1, ], ppm, shift = c(3, 4.5), backend='base')
points(peaklist[[1]]$ppm, peaklist[[1]]$Int, col = "cyan")

head(peaklist[[1]])
#>      idc      ppm       Int Etype    height       snr    curvature prominence
#> 76   926 4.267179  33135.11     1  33135.11  66.63204    -79.60716   7459.445
#> 77   971 4.253429  39609.04     1  39609.04  79.65059   -228.41090  13933.375
#> 79   993 4.246706  35544.18     1  35544.18  71.47649    -33.20873   9868.517
#> 100 1403 4.121428 111466.69     1 111466.69 224.15055  -5230.31365 100350.064
#> 101 1440 4.110123 349278.95     1 349278.95 702.37191 -18388.87714 340139.674
#> 102 1478 4.098511 346193.60     1 346193.60 696.16751 -18433.68025 335076.973