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Fit chromatographic peaks

Source: R/fit_peaks.R
fit_peaks.Rd

Peak parameters are estimated by fitting one of several models to the data using nonlinear least squares (nlsLM). Supported models include Gaussian, bidirectional exponentially modified Gaussian, or exponential-Gaussian hybrid functions. The area under each fitted curve is estimated using trapezoidal approximation.

Usage

fit_peaks(
  x,
  lambda,
  pos = NULL,
  sd_max = 50,
  fit = c("egh", "bemg", "gaussian", "raw"),
  max_iter = 1000,
  estimate_purity = TRUE,
  noise_threshold = 0.001,
  baseline = c("none", "flat", "sloped"),
  ...
)

Arguments

x

A single chromatogram in matrix format.

lambda

Wavelength at which to fit peaks. Must correspond to a wavelength present in x.

pos

Locations of peaks in vector y. If NULL, find_peaks will run automatically to find peak positions.

sd_max

Maximum width (standard deviation) for peaks. Defaults to 50.

fit

Peak model to use. Options include "bemg" (bidirectional exponentially modified Gaussian), "egh" (exponential-Gaussian hybrid), "gaussian", and "raw". If raw is selected, peaks are integrated using trapezoidal integration without model fitting. Defaults to "egh".

max_iter

Maximum number of iterations to use in nonlinear least squares peak-fitting. Defaults to 1000.

estimate_purity

Logical. Whether to estimate purity or not. Defaults to TRUE.

noise_threshold

Noise threshold. Input to get_purity.

baseline

Whether to fit a baseline offset beneath each peak model. Options are "none" (no baseline, default), "flat" (constant offset), or "sloped" (linearly varying offset). Not available when fit = "raw".

...

Additional arguments to find_peaks.

Value

A matrix with one row per peak and the following columns:

  • rt: Peak maximum location.

  • start: Peak start (only included in table if bounds = TRUE).

  • end: Peak end (only included in table if bounds = TRUE).

  • sd: Peak standard deviation.

  • tau: Exponential decay constant (only included in table if fit = "egh").

  • tau_right: Exponential decay constant for right side of peak (when bemg is selected).

  • tau_left: Exponential decay constant for left side of peak (when bemg is selected).

  • FWHM: The full width at half maximum.

  • height: Peak height above the fitted baseline.

  • area: Peak area above the fitted baseline.

  • r.squared: The R2 value for linear fit of the model to the data.

  • purity: The spectral purity of peak as assessed by get_purity.

  • floor: Constant baseline offset (only when baseline = "flat").

  • floor_start: Baseline level at the left edge of the peak window (only when baseline = "sloped").

  • floor_end: Baseline level at the right edge of the peak window (only when baseline = "sloped"). The first five elements (rt, start, end, sd and FWHM) are expressed as index positions rather than absolute retention times. The transformation to real time is done in get_peaks.

Note

The fit_peaks function is adapted from Dr. Robert Morrison's DuffyTools package as well as code published in Ron Wehrens' alsace package.

References

  • Lan, K. & Jorgenson, J. W. 2001. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks. Journal of Chromatography A 915:1-13. doi:10.1016/S0021-9673(01)00594-5 .

  • Naish, P. J. & Hartwell, S. 1988. Exponentially Modified Gaussian functions - A good model for chromatographic peaks in isocratic HPLC? Chromatographia, 26: 285-296. doi:10.1007/BF02268168 .

See also

find_peaks, get_peaks

Author

Ethan Bass

Examples

data(Sa_pr)
fit_peaks(Sa_pr[[1]], lambda = 220)
#>           rt start end        sd           tau      FWHM      height
#> 1   30.69332    14  46 6.2865644    1.20769992 14.773426   9.1034627
#> 2   50.94330    46  52 0.5711967  -11.41366848  1.342312   0.4022556
#> 3   61.44532    53  61 3.2042222    2.37308275  7.529922  14.3385995
#> 4   69.97526    61  78 2.7067311   -1.01879444  6.360818 124.1300652
#> 5   82.42709    78  85 1.3744994   -0.73109961  3.230074   2.3051668
#> 6   89.64284    85  93 1.5296385    0.61202488  3.594650   2.6256571
#> 7  104.49707    93 114 2.1826134   -0.19394678  5.129142 894.1248943
#> 8   81.84177   114 118 2.4690722   22.61770113  5.802320  42.5947951
#> 9  119.85327   118 123 5.2832737  -13.86056689 12.415693   8.6545653
#> 10 131.85675   123 139 1.8315236    0.11513594  4.304081 468.1212567
#> 11 141.10828   139 147 4.1299082   -4.37157201  9.705284   8.4526758
#> 12 156.09501   149 161 1.7963783   -0.01487998  4.221489   7.1019209
#> 13 167.73853   161 171 1.6517982   -0.14556475  3.881726  28.2608430
#> 14 183.22815   171 188 2.0807233   -0.22145455  4.889700 414.6928515
#> 15 193.98654   188 200 2.4682084   -1.29245512  5.800290 126.0967365
#> 16 216.44045   200 228 1.8375563   -0.13007408  4.318257 433.2796803
#> 17 234.50440   228 238 1.9619252   -0.17648212  4.610524  47.8442003
#> 18 243.58113   238 254 4.9483859    0.66568143 11.628707  14.0416866
#> 19 262.00099   254 264 1.8302984   -0.98597515  4.301201  19.1541885
#> 20 272.87432   264 279 3.0837104    0.05107119  7.246719  94.1813171
#> 21 284.45995   279 293 1.8712197   -0.34947351  4.397366 161.7599016
#> 22 298.28530   293 303 2.0217365   -0.90317976  4.751081  17.1078695
#> 24 320.15708   315 323 1.2587749    0.34042184  2.958121   0.9339542
#> 25 336.89949   323 347 2.2339189   -0.82019092  5.249709 171.5472176
#> 26 351.82167   347 363 4.3854006    2.73641711 10.305691   6.9880680
#> 27 379.01651   363 383 9.6193330  -13.36671566 22.605432   3.8160109
#> 28 389.96461   383 390 0.4505398  -11.19848606  1.058768   5.7371410
#> 29 396.32753   390 401 7.3086188   -2.14825864 17.175254   6.4654057
#> 30 410.94947   401 411 1.7808715 -123.44165218  4.185048   5.7088185
#> 31 419.42472   411 421 4.8293966  -14.83514636 11.349082   7.7061414
#>           area r.squared     purity
#> 1   141.237161 0.9869708 0.63636364
#> 2     1.664893 0.7267476 1.00000000
#> 3    37.107139 0.9997068 1.00000000
#> 4   846.567716 0.9954198 0.17647059
#> 5     7.964953 0.9529150 1.00000000
#> 6     9.667361 0.9974965 1.00000000
#> 7  4895.364758 0.9991512 0.08333333
#> 8    38.579138 0.8292605 0.60000000
#> 9    38.911532 0.9637970 1.00000000
#> 10 2149.558127 0.9991802 0.15384615
#> 11   46.615211 0.9910774 1.00000000
#> 12   31.861289 0.9960339 1.00000000
#> 13  114.667078 0.9997472 0.90909091
#> 14 2149.492159 0.9987345 0.15384615
#> 15  759.917479 0.9870224 0.18181818
#> 16 1996.653868 0.9988400 0.50000000
#> 17  227.707869 0.9889112 0.72727273
#> 18  150.579316 0.8325459 0.52941176
#> 19   84.009309 0.9912112 0.63636364
#> 20  707.817033 0.9118992 0.46666667
#> 21  755.914103 0.9843055 0.26666667
#> 22   85.445828 0.9455491 0.72727273
#> 24    2.857647 0.9897500 1.00000000
#> 25  972.589353 0.9950354 0.33333333
#> 26   71.516308 0.7701393 1.00000000
#> 27   63.064242 0.9955775 1.00000000
#> 28   29.703398 0.9392470 1.00000000
#> 29   64.730873 0.8411157 1.00000000
#> 30   54.811944 0.8662737 1.00000000
#> 31   66.589250 0.8950062 1.00000000