batch_2DCOW {RGCxGC}

Two-dimensional COW in batch.

Description

'batch_2DCOW' perform two-dimensional correlation optimized warping alignment in batch.

Usage

batch_2DCOW(reference, sample_chroms, segments, max_warp, add_ref = FALSE)

Arguments

reference

a GCxGC chromatogram which will be taken as the reference chromatogram.

sample_chroms

a named list with the sample chromatograms which will be aligned against to the reference chromatogram.

segments

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

max_warp

a two integer vector with the maximum warping parameter for the first and second dimension

add_ref

a logical indicating if the reference chromatogram will be joined together with the sample chromatograms. By the fault add_ref = F. If add_ref is set to T, the provide reference chromatogram will be included as another sample chromatogram in the downstream analysis.

Details

The first argument is the reference chromatogram which other chromatograms will aligned against to. Then, a named list is needed for the sample_chroms argument. Each chromatogram in this list will be aligned using the reference chromatogram. By default, the reference chromatogram will be not included in the subsequent analysis, such as MPCA. If you would like to add the reference chromatogram, then add_ref = T.

This is an adaptation of two-dimensional COW alignment, firstly implemented in MATLAB. This function takes a set of samples chromatogram to be aligned against to the reference. The argument [segment] will be used to split the whole chromatogram in n and m parts in the first and the second dimension, respectively. The [max_warp] argument provides the maximum tolerance of the signal transformation for the first and the second dimension, respectively.

Examples

# Read Sample chromatogram
GB08_fl <- system.file("extdata", "08GB.cdf", package = "RGCxGC")
MTBLS08 <- read_chrom(GB08_fl, mod_time = 5)

# Read reference chromatogram
GB09_fl <- system.file("extdata", "09GB.cdf", package = "RGCxGC")
MTBLS09 <- read_chrom(GB09_fl, mod_time = 5)

# Create a named list
# MTBLS08 will be repeated for exemplification
# Considerer that chromatograms are renamed considering the list names
batch_samples <- list(Chrom1 = MTBLS08, Chrom2 = MTBLS08)


# Perform batch 2DCOW alignment
# Add the reference chromatogram as another sample
batch_alignment <- batch_2DCOW(MTBLS09, batch_samples,
                               c(10, 40), c(1, 10), add_ref = TRUE)
# Exclude the reference chromatogram in the sample chromatogram set
batch_alignment <- batch_2DCOW(MTBLS09, batch_samples, c(10, 40), c(1, 10))