Correct peak positions according to a PTW warping model

Corrects retention time differences in peak_list using parametric time warping as implemented in the ptw package.

Usage

correct_peaks(peak_list, mod_list, chrom_list, match_names = TRUE)

Arguments

peak_list: A peak_list object created by get_peaks, containing a nested list of peak tables where the first level is the sample, and the second level is the spectral wavelength. Every wavelength is described by a matrix where each row corresponds to a feature, and the columns contain information on that feature (e.g., retention time, peak width (FWHM), height, area, etc.)
mod_list: A list of ptw models.
chrom_list: List of chromatograms from which the ptw models are derived.
match_names: Logical. Whether to actively match the names of the peak_list to the list of models (mod_list). Defaults to TRUE.

Value

The input list of peak tables is returned with extra columns containing the corrected retention times.

Details

Once an appropriate warping model has been established, corrected retention times can be predicted for each peak. These are stored in a separate column in the list of peak tables.

Note

This function is adapted from the correctPeaks function in the alsace package by Ron Wehrens: https://github.com/rwehrens/alsace/blob/master/R/correctPeaks.R.

Author

Ron Wehrens, Ethan Bass

Examples

if (FALSE) { # interactive()
data(Sa_pr)
warp <- correct_rt(chrom_list = Sa_pr, lambdas = 210, what = "models")
pks <- get_peaks(Sa_pr, lambda = "210")
correct_peaks(pks, mod_list = warp, chrom_list = Sa_pr)
}