This package provides code to determine from GWAS data whether observed clinical heterogeneity in a disease phenotype corresponds to differing genetic bases of disease. Disease heterogeneity is characterised either by a division of the case group into two subtypes or by a single quantitative variable. Our overall approach is to compute two Z-scores, one comparing cases with controls and the other characterising phenotypic heterogeneity without accounting for controls. We then test for the presence of a set of SNPs which show evidence of association both with case/control status and subgroup status. Given evidence of differential genetic bases, we then provide functions to attempt to determine the SNPs responsible for the observed difference. Further information can be found in our paper at http://biorxiv.org/content/early/2016/08/02/037713.
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