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maldi_PIKE — Peak Information KErnel for MALDI-TOF MS spectra

maldi_PIKE is a small library for Python 3 that include the code used for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'. The main method includes PIKE, the Peak Information KErnel for MALDI-TOF MS spectra, embedded in a Gaussian Process. We developed PIKE based on heat diffusion on structured objects. It is well suited for MALDI-TOF mass spectra and able to capture interactions between mass peaks.

Dependencies

  • Python 3.7
  • packages listed in pyproject.toml

Installation

  • Clone the repository
  • poetry install

Follow the instructions given by poetry.

Example behaviour of PIKE

Figure 2:

PIKE_behaviour

Code to recreate this graphic in matplotlib can be found in ismb2020_maldi/visualise_feature_map.py. Use the script as follows:

poetry run python ismb2020_maldi/visualise_feature_map.py data/Example_peaks.txt

This should result in the following plot:

PIKE_behaviour_matplotlib

This repository is work in progress.

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Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'

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