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bioRxiv · 10.1101/2025.03.28.645834

Orchestrating multi-state QTL analysis with Bioconductor

Del Azodi, C. B.·Dunstone, A. M.·McCarthy, D. J.
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Abstract

MotivationThe scope of many Quantitative Trait Loci (QTL) mapping studies has increased to include different cellular and environmental states. However, drawing biologically relevant conclusions from the large, high-dimensional data that come from multi-state QTL mapping studies is not straightforward. ResultsTo address this problem, we introduce two R packages, QTLExperiment and multistateQTL. The QTLExperiment package provides a robust container for storing and manipulating QTL summary statistics and associated metadata. Building upon existing Bioconductor infrastructure and conventions, this object class is consistent, user-friendly, and well-documented. The multistateQTL package introduces tools to facilitate the analysis of multi-state QTL data stored in a QTLExperiment container. This package provides methods for statistical analysis, quantification of sharing, classification of multi-state QTL associations, visualization of the data, and more. It also provides flexible methods for simulating multi-state QTL summary statistics with user-defined properties. Availability and implementationThe packages QTLExperiment and multistateQTL are available on Bioconductor (https://www.bioconductor.org/packages/QTLExperiment and https://bioconductor.org/packages/multistateQTL).

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Del Azodi, C. B., Dunstone, A. M., McCarthy, D. J.. 2025-04-01. Orchestrating multi-state QTL analysis with Bioconductor. https://doi.org/10.1101/2025.03.28.645834

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