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Align Spectra

Source: R/30_align.R
align.Rd

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 = 5, verbose = FALSE)

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. Passed as argument range to combine_peaks().

verbose

Whether to print additional information during the alignment process.

Value

An object of type align as described in metabodecon_classes.

Examples

sim_dir <- metabodecon_file("bruker/sim")
spectra <- read_spectra(sim_dir)
decons <- deconvolute(spectra, sfr = c(3.55, 3.35))
aligned <- align(decons)
aligned
#> aligns object with 16 align elements
#> sim_01: align object (2048 dp, 3.6 to 3.3 ppm, 27 peaks)
#> sim_02: align object (2048 dp, 3.6 to 3.3 ppm, 30 peaks)
#> sim_03: align object (2048 dp, 3.6 to 3.3 ppm, 25 peaks)
#> sim_04: align object (2048 dp, 3.6 to 3.3 ppm, 26 peaks)
#> sim_05: align object (2048 dp, 3.6 to 3.3 ppm, 26 peaks)
#> sim_06: align object (2048 dp, 3.6 to 3.3 ppm, 24 peaks)
#> sim_07: align object (2048 dp, 3.6 to 3.3 ppm, 29 peaks)
#> sim_08: align object (2048 dp, 3.6 to 3.3 ppm, 26 peaks)
#> sim_09: align object (2048 dp, 3.6 to 3.3 ppm, 28 peaks)
#> sim_10: align object (2048 dp, 3.6 to 3.3 ppm, 35 peaks)
#> sim_11: align object (2048 dp, 3.6 to 3.3 ppm, 29 peaks)
#> sim_12: align object (2048 dp, 3.6 to 3.3 ppm, 28 peaks)
#> sim_13: align object (2048 dp, 3.6 to 3.3 ppm, 25 peaks)
#> sim_14: align object (2048 dp, 3.6 to 3.3 ppm, 27 peaks)
#> sim_15: align object (2048 dp, 3.6 to 3.3 ppm, 29 peaks)
#> sim_16: align object (2048 dp, 3.6 to 3.3 ppm, 28 peaks)