Calculate peak purity — get_purity • chromatographR

Estimates peak purity by assessing spectral dissimilarity across the peak region, following Stahl (2003).

Usage

get_purity(
  x,
  pos,
  weight = 1,
  cutoff = 0.05,
  noise_variance = NULL,
  noise_threshold = 0.01,
  lambdas,
  try = TRUE
)

x: A chromatographic matrix (timepoints × wavelengths).
pos: A length-3 integer vector c(apex, start, end) giving the row indices of the peak apex, left boundary, and right boundary in x.
weight: Weight parameter passed to get_agilent_threshold.
cutoff: Proportion of maximum absorbance to use as cutoff. Passed to trim_peak. Defaults to 0.05.
noise_variance: Variance of noise. Passed to get_agilent_threshold.
noise_threshold: Threshold to define noise. Highest proportion of maximum absorbance. Defaults to 0.01.
lambdas: Wavelengths to include in calculations.
try: Logical. Whether to estimate the purity or not. Defaults to TRUE.

Returns the mean purity of the peak specified by pos, defined as the proportion of timepoints with purity values below 1.

Stahl, Mark. “Peak Purity Analysis in HPLC and CE Using Diode-Array Technology.” Agilent Technologies, April 1, 2003, 16. 5988-8647EN.pdf

Ethan Bass

data(Sa_warp)
x <- Sa_warp[[1]]
pos <- c(37, 22, 51)
get_purity(x, pos)
#> [1] 0.6666667