Orchestrating multi-state QTL analysis with Bioconductor

Abstract 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 ).