Python 3 implementation of maximum impact estimation (Donato et al., 2013)
Project description
Crosstalk correction
Python 3 implementation of Donato et al.’s 2013 maximum impact estimation algorithm for correcting crosstalk effects in pathway analysis.
Background
Crosstalk: Donato et al. (2013) use the term crosstalk to refer to the effect that pathways exercise on each other (in pathway analysis methods such as enrichment analysis, functional class scoring, and topology-based methods) due to the presence of overlapping genes.
Maximum impact estimation: They developed a correction method called maximum impact estimation that takes into account overlaps between pathways. The approach infers an underlying pathway impact matrix where each gene only contributes to one pathway using an expectation maximization technique.
PathCORE: The crosstalk correction method is used in the PathCORE software, a hypothesis generation tool that identifies co-occurring pathways from the results of an unsupervised analysis of transcriptomic data. Due to confusion around the term “crosstalk,” we refer to this procedure as “overlap-correction” in the PathCORE software and paper.
Installation
Please use Python 3.4 or higher. To install the current PyPI version (recommended), run:
pip install crosstalk-correction
For the latest GitHub version, run:
pip install git+https://github.com/kathyxchen/crosstalk-correction.git#egg=crosstalk-correction
Package contents
crosstalk_correction.py
crosstalk_correction.py contains the implementation of the crosstalk correction procedure. The crosstalk_correction function wraps the maximum impact estimation algorithm (in maximum_impact_estimation) and reduces the number of pre/post-processing steps required to run/interpret the results of maximum_impact_estimation.
We recommend that crosstalk_correction be used directly, but the functions called within crosstalk_correction have also been documented so that users can determine how to best address their use case.
Acknowledgements
This work was supported by the Penn Institute for Bioinformatics
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