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Align Signals using 'speaq'

Source: R/30_align.R
speaq_align.Rd

Performs signal alignment across the individual spectra using the 'speaq' package (Beirnaert C, Meysman P, Vu TN, Hermans N, Apers S, Pieters L, et al. (2018) speaq 2.0: A complete workflow for high-throughput 1D NMRspectra processing and quantification. PLoS Comput Biol 14(3): e1006018. https://www.doi.org/10.1371/journal.pcbi.1006018). The spectra deconvolution process yields the signals of all spectra. Due to slight changes in measurement conditions, e.g. pH variations, signal positions may vary slightly across spectra. As a consequence, prior to further analysis signals belonging to the same compound have to be aligned across spectra. This is the purpose of the 'speaq' package.

Usage

speaq_align(
  feat = gen_feat_mat(spectrum_data),
  maxShift = 50,
  spectrum_data = generate_lorentz_curves_sim(),
  si_size_real_spectrum = length(spectrum_data[[1]]$y_values),
  verbose = TRUE,
  show = FALSE,
  mfrow = c(2, 1)
)

Arguments

feat

Output of gen_feat_mat().

maxShift

Maximum number of points along the "ppm-axis" which a value can be moved by speaq package e.g. 50. 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.

spectrum_data

Output of generate_lorentz_curves().

si_size_real_spectrum

Number of real data points in your original spectra.

verbose

Whether to print additional information during the alignment process.

show

Whether to plot the original and aligned spectra.

mfrow

Layout to use for the plot. Passed on to par(). Use mfrow = NULL if the plot layout should not be changed.

Value

A matrix containing the integral values of the spectra after alignment.

There is one row per spectrum and one column per ppm value. The entry at position i, j holds the integral value of the signal from spectrum i that has its center at position j after alignment by speaq. If there is no signal with center j in spectrum i, entry i, j is set to NA. The column names of the matrix are the ppm values of the original spectra.

Example return matrix:

    ...  3.59  3.55  3.57  3.56  3.55  3.54  3.53
  .----------------------------------------------> PPM
1 | NA   NA    0.20  NA    NA    NA    0.25  NA
2 | NA   NA    0.15  NA    NA    NA    0.13  NA
3 | NA   NA    NA    0.2   NA    NA    0.18  NA
SpNr

Author

Initial version from Wolfram Gronwald. Refactored by Tobias Schmidt in 2024.

Examples

sim_subset <- metabodecon_file("bruker/sim_subset")
spectrum_data <- generate_lorentz_curves_sim(sim_subset)
feat <- gen_feat_mat(spectrum_data)
maxShift <- 200
M <- speaq_align(feat, maxShift, spectrum_data, show = TRUE)
#> 
#>  --------------------------------
#>  dohCluster will run with maxShift= 200
#>  If you want dohCluster to detect the optimal maxShift automatically,
#>  use dohCluster(..., maxShift = NULL, ...)
#>  --------------------------------
#> 
#>  aligning spectrum  1
#>  Median pearson correlation of aligned spectra: 0.9977223
#>  Alignment time:  2e-04  minutes

str(M)
#>  num [1:2, 1:2048] NA NA NA NA NA NA NA NA NA NA ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : NULL
#>   ..$ : chr [1:2048] "3.59" "3.58985" "3.5897" "3.58955" ...