robustica: customizable robust independent component analysis

Anglada-Girotto, Miquel; Miravet Verde, Samuel, 1992-; Serrano Pubull, Luis, 1982-; Head, Sarah A.

doi:http://dx.doi.org/10.1186/s12859-022-05043-9

robustica: customizable robust independent component analysis

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Anglada-Girotto M, Miravet-Verde S, Serrano L, Head SA. robustica: customizable robust independent component analysis. BMC Bioinformatics. 2022 Dec 5;23(1):519. DOI: 10.1186/s12859-022-05043-9

Abstract

Background: Independent Component Analysis (ICA) allows the dissection of omic datasets into modules that help to interpret global molecular signatures. The inherent randomness of this algorithm can be overcome by clustering many iterations of ICA together to obtain robust components. Existing algorithms for robust ICA are dependent on the choice of clustering method and on computing a potentially biased and large Pearson distance matrix. Results: We present robustica, a Python-based package to compute robust independent components with a fully customizable clustering algorithm and distance metric. Here, we exploited its customizability to revisit and optimize robust ICA systematically. Of the 6 popular clustering algorithms considered, DBSCAN performed the best at clustering independent components across ICA iterations. To enable using Euclidean distances, we created a subroutine that infers and corrects the components' signs across ICA iterations. Our subroutine increased the resolution, robustness, and computational efficiency of the algorithm. Finally, we show the applicability of robustica by dissecting over 500 tumor samples from low-grade glioma (LGG) patients, where we define two new gene expression modules with key modulators of tumor progression upon IDH1 and TP53 mutagenesis. Conclusion: robustica brings precise, efficient, and customizable robust ICA into the Python toolbox. Through its customizability, we explored how different clustering algorithms and distance metrics can further optimize robust ICA. Then, we showcased how robustica can be used to discover gene modules associated with combinations of features of biological interest. Taken together, given the broad applicability of ICA for omic data analysis, we envision robustica will facilitate the seamless computation and integration of robust independent components in large pipelines.