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April 1st, 2025
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St. Vincent\\\'s Institute of Medical Research
bioinformatics
biorxiv

Orchestrating multi-state QTL analysis with Bioconductor

Del Azodi, C. B.Open in Google Scholar•Dunstone, A. M.Open in Google Scholar•McCarthy, D. J.Open in Google Scholar

Motivation: The 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. Results: To 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 implementation: The packages QTLExperiment and multistateQTL are available on Bioconductor (https://www.bioconductor.org/packages/QTLExperiment and https://bioconductor.org/packages/multistateQTL).

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