FracFixR: A compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data

Abstract

MotivationRNA fractionation followed by sequencing is widely used to study RNA localization, translation, and subcellular compartmentalization. Interpreting fractionated RNA-seq data poses a fundamental compositional challenge: library preparation and sequencing depth obscure the original proportions of RNA fractions, which can bias comparisons - particularly when biological changes shift RNA distribution across fractions. This bias compromises comparisons of fraction-specific RNA profiles and limits the utility of standard differential expression methods. Existing approaches using transcript frequency ratios or standard normalization fail to account for the compositional nature of fractionated samples and cannot estimate the unrecoverable "lost" fraction. ResultsWe developed FracFixR, a statistical framework that reconstructs original fraction proportions by modeling the compositional relationship between whole and fractionated RNA samples. Using non-negative linear regression on carefully selected transcripts, FracFixR estimates global fraction weights, corrects individual transcript frequencies, and quantifies unrecoverable material. The framework includes methods for differential proportion testing between conditions using binomial GLM, logit, or beta-binomial models. We rigorously validated FracFixR using synthetic data with known ground truth and real polysome profiling data from multiple cell lines, demonstrating accurate reconstruction of fraction weights (Pearson correlation > 0.85) and enabling detection of differentially translated transcripts between cancer subtypes. Availability and implementationFracFixR is implemented as an R package freely available on GitHub at https://github.com/Arnaroo/FracFixR.