pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R

• Published in: Briefings in functional genomics Vol. 24
• Main Authors: Kolisnik, Tyler, Keshavarz-Rahaghi, Faeze, Purcell, Rachel V, Smith, Adam N H, Silander, Olin K
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 07.10.2024
• Subjects: Algorithms; Data Analysis; Genomics - methods; Humans; Random Forest; Review Paper; Software; biomarker identification; random forest; machine learning; genomic data analysis; bioinformatics
• ISSN: 2041-2649; 2041-2657; 2041-2647; 2041-2657
• DOI: 10.1093/bfgp/elae038

Abstract Random Forest models are widely used in genomic data analysis and can offer insights into complex biological mechanisms, particularly when features influence the target in interactive, nonlinear, or nonadditive ways. Currently, some of the most efficient Random Forest methods in terms of computational speed are implemented in Python. However, many biologists use R for genomic data analysis, as R offers a unified platform for performing additional statistical analysis and visualization. Here, we present an R package, pyRforest, which integrates Python scikit-learn “RandomForestClassifier” algorithms into the R environment. pyRforest inherits the efficient memory management and parallelization of Python, and is optimized for classification tasks on large genomic datasets, such as those from RNA-seq. pyRforest offers several additional capabilities, including a novel rank-based permutation method for biomarker identification. This method can be used to estimate and visualize P-values for individual features, allowing the researcher to identify a subset of features for which there is robust statistical evidence of an effect. In addition, pyRforest includes methods for the calculation and visualization of SHapley Additive exPlanations values. Finally, pyRforest includes support for comprehensive downstream analysis for gene ontology and pathway enrichment. pyRforest thus improves the implementation and interpretability of Random Forest models for genomic data analysis by merging the strengths of Python with R. pyRforest can be downloaded at: https://www.github.com/tkolisnik/pyRforest with an associated vignette at https://github.com/tkolisnik/pyRforest/blob/main/vignettes/pyRforest-vignette.pdf.