msalign: Signal calibration and alignment by reference peaks
msalign - signal calibration and alignment
This package was inspired by MATLAB's msalign function which allows alignment of multiple signals to reference peaks.
Install from PyPi
pip install msalign
Install directly from GitHub
pip install -e git+https://github.com/lukasz-migas/msalign.git
Install in development mode
python setup.py develop
Usage is relatively straightforward. Simply import
msalign from the package and provide
msalign accepts a lot of other parameters that might improve your alignment - simply provide them
import numpy as np from msalign import msalign filename = r"./example_data/msalign_test_data.csv" data = np.genfromtxt(filename, delimiter=",") x = data[1:, 0] array = data[1:, 1:].T peaks = [3991.4, 4598, 7964, 9160] aligned = msalign(x, array, peaks, weights=[60, 100, 60, 100], only_shift=False)
Zoom-in on each peak the spectrum was aligned against
Monchamp, P., Andrade-Cetto, L., Zhang, J.Y., and Henson, R. (2007) Signal Processing Methods for Mass Spectrometry. In Systems Bioinformatics: An Engineering Case-Based Approach, G. Alterovitz and M.F. Ramoni, eds. Artech House Publishers).
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