speaq_align
speaq_align.RdAlignment by speaq. The speaq package is used to perform the signal alignment across the individual spectra. For speaq please cite: (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.
Arguments
- feat
(data frame) Contains data of the deconvoluted signals of all analyzed spectra before alignment.
- maxShift
(positive integer) 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
(data frame) The output generated by the function generate_lorentz_curves.
- si_size_real_spectrum
(positive integer) number of real data points in your original spectra, e.g. 128k = 131072 data points
Details
The output of speaq_align is a data matrix of aligned integral values. Each row contains the data of each spectrum and each column corresponds to one data point. Each entry corresponds to the integral of a deconvoluted signal with the signal center at this specific position after alignment by speaq.