cILR: Competitive isometric log-ratio for taxonomic enrichment analysis
Research in human associated microbiomes often involves the analysis of taxonomic count tables generated via high-throughput sequencing. It is difficult to apply statistical tools as the data is high-dimensional, sparse, and strictly compositional. An approachable way to alleviate high-dimensionality and sparsity is to aggregate variables into pre-defined sets. Set-based analysis is ubiquitous in the genomics literature, and has demonstrable impact in improving interpretability and power of
... stream analysis. Unfortunately, there is a lack of sophisticated set-based analysis methods specific to microbiome taxonomic data, where current practice often employs abundance summation as a technique for aggregation. This approach prevents comparison across sets of different sizes, does not preserve inter-sample distances, and amplifies protocol bias. Here, we attempt to fill this gap with a new single sample taxon set enrichment method based on the isometric log ratio transformation and the competitive null hypothesis commonly used in the enrichment analysis literature. Our approach, titled competitive isometric log ratio (cILR), generates sample-specific enrichment scores as the scaled log ratio of the subcomposition defined by taxa within a set and the subcomposition defined by its complement. We provide sample-level significance testing by estimating an empirical null distribution of our test statistic with valid p-values. Herein we demonstrate using both real data applications and simulations that cILR controls for type I error even under high sparsity and high inter-taxa correlation scenarios. Additionally, it provides informative scores that can be inputs to downstream differential abundance and prediction tasks.