correct_rt: Correct retention time

In chromatographR: Chromatographic Data Analysis Toolset

Correct retention time

Description

Aligns chromatograms using parametric time warping, as implemented in ptw, or variable penalty dynamic time warping, as implemented in VPdtw.

Usage

correct_rt(
  chrom_list,
  lambdas,
  models = NULL,
  reference = "best",
  alg = c("ptw", "vpdtw"),
  what = c("corrected.values", "models"),
  init.coef = c(0, 1, 0),
  n.traces = NULL,
  n.zeros = 0,
  scale = FALSE,
  trwdth = 200,
  plot = FALSE,
  penalty = 5,
  maxshift = 50,
  verbose = FALSE,
  ...
)

Arguments

chrom_list	List of matrices containing concentration profiles.
lambdas	Select wavelengths to use by name.
models	List of models to warp by.
reference	Index of the sample that is to be considered the reference sample.
alg	algorithm to use: parametric time warping (ptw) or variable penalty dynamic time warping (vpdtw).
what	What to return: either the 'corrected.values' (useful for visual inspection) or the warping 'models' (for further programmatic use).
init.coef	Starting values for the optimization.
n.traces	Number of traces to use.
n.zeros	Number of zeros to add.
scale	Logical. If true, scale chromatograms before warping.
trwdth	width of the triangle in the WCC criterion.
plot	Logical. Whether to plot alignment.
penalty	The penalty for VPdtw is calculated by dividing the dilation by the number provided by this argument. Thus, a lower number allows more warping to occur. Defaults to 5.
maxshift	Integer. Maximum allowable shift for VPdtw.
verbose	Whether to be verbose.
...	Optional arguments for the ptw function. The only argument that cannot be changed is warp.type: this is always equal to "global".

Details

To use variable penalty dynamic time warping, the VPdtw package must be manually installed: install.packages('VPdtw').

Value

A list of ptw objects or a list of warped absorbance profiles, depending on the value of the what argument.

Note

Adapted from correctRT function in the alsace package by Ron Wehrens.

Author(s)

Ethan Bass

References

• Clifford, D., Stone, G., Montoliu, I., Rezzi, S., Martin, F. P., Guy, P., Bruce, S., & Kochhar, S. 2009. Alignment using variable penalty dynamic time warping. Analytical chemistry, 81(3):1000-1007. doi: 10.1021/ac802041e.

• Clifford, D., & Stone, G. 2012. Variable Penalty Dynamic Time Warping Code for Aligning Mass Spectrometry Chromatograms in R. Journal of Statistical Software, 47(8):1-17. doi: 10.18637/jss.v047.i08.

• Eilers, P.H.C. 2004. Parametric Time Warping. Anal. Chem., 76:404-411. doi: 10.1021/ac034800e.

• Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. Fast parametric time warping of peak lists. Bioinformatics, 31:3063-3065. doi: 10.1093/bioinformatics/btv299.

• Wehrens, R., Carvalho, E., Fraser, P.D. 2015. Metabolite profiling in LC–DAD using multivariate curve resolution: the alsace package for R. Metabolomics, 11:143-154. doi: 10.1007/s11306-014-0683-5

See Also

ptw, correct_peaks, VPdtw

Examples

data(Sa_pr)
warping.models <- correct_rt(Sa_pr, what = "models", lambdas=c("210"))
warp <- correct_rt(chrom_list = Sa_pr, models = warping.models)

chromatographR documentation built on Aug. 24, 2022, 9:06 a.m.