gJLS2: an R package for generalized joint location and scale analysis in X-inclusive genome-wide association studies

A joint analysis of location and scale can be a powerful tool in genome-wide association studies to uncover previously overlooked markers that influence a quantitative trait through both mean and variance, as well as to prioritize candidates for gene–environment interactions. This approach has recently been generalized to handle related samples, dosage data, and the analytically challenging X-chromosome. We disseminate the latest advances in methodology through a user-friendly R software package with added functionalities to support genome-wide analysis on individual-level or summary-level data. The implemented R package can be called from PLINK or directly in a scripting environment, to enable a streamlined genome-wide analysis for biobank-scale data. Application results on individual-level and summary-level data highlight the advantage of the joint test to discover more genome-wide signals as compared to a location or scale test alone. We hope the availability of gJLS2 software package will encourage more scale and/or joint analyses in large-scale datasets, and promote the standardized reporting of their P-values to be shared with the scientific community.