CPBayes {CPBayes}

CPBayes: An R-package implemeting a Bayesian meta analysis method for studying cross-phenotype genetic associations.

Description

Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy). CPBayes is a Bayesian meta analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes is based on a spike and slab prior.

Details

The package consists of following functions: analytic_locFDR_BF_uncor, cpbayes_uncor; analytic_locFDR_BF_cor, cpbayes_cor; post_summaries, forest_cpbayes, estimate_corln.

Functions

analytic_locFDR_BF_uncor

It analytically computes the local FDR (locFDR) and Bayes factor (BF) quantifying the evidence of aggregate-level pleiotropic association for uncorrelated summary statistics.

cpbayes_uncor

It implements CPBayes (based on MCMC) for uncorrelated summary statistics to figure out the optimal subset of non-null traits underlying a pleiotropic signal and other insights. The summary statistics across traits/studies are uncorrelated when the studies have no overlapping/genetically related subjects.

analytic_locFDR_BF_cor

It analytically computes the local FDR (locFDR) and Bayes factor (BF) for correlated summary statistics.

cpbayes_cor

It implements CPBayes (based on MCMC) for correlated summary statistics to figure out the optimal subset of non-null traits underlying a pleiotropic signal and other insights. The summary statistics across traits/studies are correlated when the studies have overlapping/genetically related subjects or the phenotypes were measured in a cohort study.

post_summaries

It summarizes the MCMC data produced by cpbayes_uncor or cpbayes_cor. It computes additional summaries to provide a better insight into a pleiotropic signal. It works in the same way for both cpbayes_uncor and cpbayes_cor.

forest_cpbayes

It creates a forest plot presenting the pleiotropy result obtained by cpbayes_uncor or cpbayes_cor. It works in the same way for both cpbayes_uncor and cpbayes_cor.

estimate_corln

It computes an approximate correlation matrix of the beta-hat vector for multiple overlapping case-control studies using the sample-overlap count matrices.

References

Majumdar A, Haldar T, Bhattacharya S, Witte JS (2018) An efficient Bayesian meta analysis approach for studying cross-phenotype genetic associations. PLoS Genet 14(2): e1007139.