Align Spectra — align • metabodecon

Align signals across a list of deconvoluted spectra using the 'CluPA' algorithm from the 'speaq' package, described in Beirnaert et al. (2018) doi:10.1371/journal.pcbi.1006018 and Vu et al. (2011) doi:10.1186/1471-2105-12-405 plus the additional peak combination described in combine_peaks().

Usage

align(
  x,
  maxShift = 50,
  maxCombine = 0,
  verbose = TRUE,
  method = 2,
  install_deps = NULL,
  nworkers = 1,
  ref = NULL,
  full = TRUE
)

Arguments

x: An object of type decons1 or decons2 as described in Metabodecon Classes. To align decons0 objects (as returned by the now deprecated MetaboDecon1D), you can use as_decons2() to convert it to a decons2 object first.
maxShift: Maximum number of points along the "ppm-axis" a value can be moved by the 'speaq' package. 50 is a suitable starting value for plasma spectra with a digital resolution of 128K. Note that this parameter has to be individually optimized depending on the type of analyzed spectra and the digital resolution. For urine which is more prone to chemical shift variations this value most probably has to be increased. Passed as argument maxShift to speaq_align().
maxCombine: Amount of adjacent columns which may be combined for improving the alignment during the CluPA step. We recommend setting this to 0 and instead relying on the peak snapping implemented in get_si_mat(). Since version 1.7.0 the default is 0. Non-zero values are deprecated and support will be removed in a future version.
verbose: Whether to print additional information during the alignment process.
method: Alignment backend. 1: use the original implementation from the 'speaq' package. 2 (default): use metabodecon's built-in reimplementation of the CluPA algorithm. 3: use metabodecon's peak-based pairwise alignment, which works directly on the deconvoluted peak parameters (x0, lambda, A). Method 3 is experimental and must not be used in production. It is very likely to change in non-backwards-compatible ways over the next few weeks.
install_deps: Only used when method = 1. 'speaq' relies on the 'MassSpecWavelet' and 'impute' packages. Both, 'MassSpecWavelet' and 'impute' are not available on CRAN, but can be installed from Bioconductor or R-Universe. If install_deps=TRUE, these packages will be automatically installed from R-Universe without asking for confirmation. If install_deps=NULL (default), the user will be asked for confirmation before installing missing dependencies. If asking for confirmation is not possible or install_deps=FALSE, the function will raise an error if the packages are not installed.
nworkers: Number of parallel workers for the alignment. Default is 1 (no parallelism).
ref: Optional reference spectrum of type align or decon2. When supplied, all spectra in x are aligned towards this reference. The reference is prepended to x internally and removed from the result. If NULL (default), the reference is chosen automatically via speaq::findRef().
full: If TRUE (default), store the full aligned Lorentz-curve superposition in each returned spectrum. If FALSE, skip that reconstruction step to save time and memory. Skipping reconstruction of the superposition means the plotting routines will not work as expected, so only use full=FALSE if you are sure you don't need the superposition.

Value

An object of type align as described in Metabodecon Classes.

Author

2024-2025 Tobias Schmidt: initial version.

Examples

if (interactive()) {
    # Example requires an interactive R session, because in case of missing
    # dependencies the user will be asked for confirmation to install them.
    decons <- deconvolute(sim[1:2], sfr = c(3.55, 3.35))
    aligned <- align(decons)
}