chromatographR (version 0.4.4)

correct_rt: 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,
  ...
)

Value

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

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".

Author

Ethan Bass

Details

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

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. tools:::Rd_expr_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. tools:::Rd_expr_doi("10.18637/jss.v047.i08").

• Eilers, P.H.C. 2004. Parametric Time Warping. Anal. Chem., 76:404-411. tools:::Rd_expr_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. tools:::Rd_expr_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. tools:::Rd_expr_doi("10.1007/s11306-014-0683-5")

See Also

ptw, correct_peaks, VPdtw

Examples

if (FALSE) { # interactive()
data(Sa_pr)
warping.models <- correct_rt(Sa_pr, what = "models", lambdas=c("210"))
warp <- correct_rt(chrom_list = Sa_pr, models = warping.models)
}