condFDR-package: condFDR: a package for calculating conditional and...

In alexploner/condFDR: Conditional and conjunctional false discovery rate

Description

Given a suitably pruned set of SNPs with p-values for two distinct phenotypes, the conditional FDR can be used to provide improved multiple-testing adjusted inference for the genetic associations for one phenotype, conditional on the associations seen for the second phenotype. In the same setting, the conjuncational FDR can be used to provide improved and adjusted inference for SNPs that are associated with both phenotypes (Andreassen et al., 2013; Smeland et al., 2020).

Functionality

This package provides two functions, cFDR and ccFDR, that implement the conditional and conjunctional FDR, respectively.

References

• Andreassen OA et al (2013) Improved detection of common variants associated with schizophrenia by leveraging pleiotropy with cardiovascular-disease risk factors. Am J Hum Genet 92:197–209. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567279/

• Smeland OB et al (2020) Discovery of shared genomic loci using the conditional false discovery rate approach. Human Genetics (2020) 139:85–94 https://doi.org/10.1007/s00439-019-02060-2

alexploner/condFDR documentation built on Dec. 31, 2020, 7:43 p.m.