twod_cow {RGCxGC}

Two-dimensional correlation optimized warping alignment

Description

This is an adaptation of two-dimesional COW alignment, first implemented in MATLAB (Tomasi et al. 2004). This functions takes a sample chromatogram to be aligned against a reference. The argument [segment] will be used to split the whole chromatogram in n and m parts the first and the second dimension, respectively. The [max_warp] argument provides de maximum tolerance of the signal transformation for the first and the second dimension (Dabao Zhang et al. 2008).

Usage

twod_cow(sample_chrom, ref_chrom, segments, max_warp)

Arguments

sample_chrom

A GCxGC class chromatogram imported by read_chrom function or a preprocessed chromatogram.

ref_chrom

A representative GCxGC chromatogram chosen to be the template which sample_chrom will be aligned.

segments

A two integer vector with number of segments which the first and second dimension will be divided, respectively.

max_warp

A two integer vector with the maximum warping parameter.

References

Dabao Zhang, Xiaodong Huang, Fred E. Regnier, Min Zhang (2008). “Two-dimensional correlation optimized warping algorithm for aligning GCxGC-MS data.” Analytical Chemistry, 80(8), 2664–2671.

Tomasi G, Van Den Berg F, Andersson C (2004). “Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data.” Journal of Chemometrics, 18(5), 231–241.

Examples

GB08_fl <- system.file("extdata", "08GB.cdf", package = "RGCxGC")
GB09_fl <- system.file("extdata", "09GB.cdf", package = "RGCxGC")
GB08 <- read_chrom(GB08_fl, 5L)
GB09 <- read_chrom(GB09_fl, 5L)

GB09_al <- twod_cow(sample_chrom = GB09, ref_chrom = GB08,
                    segments = c(20, 40), max_warp = c(2, 8))