Calculate purity thresholds — get_agilent_threshold • chromatographR

Computes the threshold used by get_purity: the similarity expected between a spectrum and the reference if they differed only by noise, the product of their reliabilities \((1 - \sigma^2_{noise} / \sigma^2_i)(1 - \sigma^2_{noise} / \sigma^2_{ref})\), capped at max_threshold.

Usage

get_agilent_threshold(
  x,
  pos,
  noise_inflation = 1,
  noise_variance = NULL,
  noise_method = c("quantile", "threshold"),
  noise_quantile = 0.1,
  noise_window = NULL,
  noise_threshold = NULL,
  max_threshold = 0.99,
  background_correction = c("linear", "constant", "none"),
  reference = c("average", "apex"),
  cutoff = 0.05,
  lambdas,
  weight = NULL
)

Arguments

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.
noise_inflation: Multiplier applied to the noise variance. Defaults to 1.
noise_variance: Variance of noise.
noise_method: How to select the timepoints used to estimate the noise variance. Either "quantile" or "threshold".
noise_quantile: Quantile of maximum absorbance below which timepoints are treated as noise.
noise_window: Optional range of row indices to use as the noise region.
noise_threshold: Threshold to define noise. Used only when noise_method == "threshold", where NULL (the default) means 0.005.
max_threshold: Ceiling on the threshold. Defaults to 0.99.
background_correction: How to correct the peak spectra for background absorbance. Either "linear", "constant", or "none".
reference: Which spectrum to compare against. Either "average" (the default) or "apex". See get_purity.
cutoff: Proportion of the corrected apex height below which timepoints are excluded from the average reference spectrum. Defaults to 0.05.
lambdas: Wavelengths to include. Character values are matched to the column names of x; numeric values are taken as column indices.
weight: The weight argument is deprecated. Please use noise_inflation instead.

Value

Returns a vector of purity thresholds, one for each timepoint from the start to the end of the peak specified by pos, or NULL if the peak cannot be assessed.

References

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

Author

Ethan Bass

Examples

data(Sa_warp)
x <- Sa_warp[[1]]
pos <- c(37, 22, 51)
get_agilent_threshold(x, pos)
#>  [1] 0.0000000 0.0000000 0.0000000 0.0000000 0.6221288 0.8321277 0.9184135
#>  [8] 0.9579810 0.9755804 0.9831036 0.9863842 0.9878527 0.9885007 0.9887190
#> [15] 0.9886271 0.9881708 0.9870904 0.9847495 0.9795133 0.9667497 0.9359573
#> [22] 0.8829043 0.8173311 0.7015591 0.4184964 0.0000000 0.0000000 0.0000000
#> [29] 0.0000000 0.0000000