GEEaSPU (version 1.0.2)

GEEaSPU-package: Adaptive Association Tests for Multiple Phenotypes using Generalized Estimating Equations (GEE)

Description

Provides adaptive association tests for SNP level, gene level and pathway level analyses.

Details

Functions for adaptive association tests including GEEaSPU, GEEaSPUset and GEEaSPUpath. These methods use a weighting scheme for testing associations with multiple phenotypes. GEEaSPU function computes a SNP level p value; GEEaSPUset function can be used for the SNP-set (gene) level association test, while GEEaSPUpath function is for the gene-set (pathway) level analysis.

References

Kim J, Zhang Y, and Pan W (2016). "Powerful and adaptive testing for multi-trait and multi-SNP associations with GWAS and sequencing data." Genetics 203(2), 715--731.

Zhang Y, Xu Z, Shen, X and Pan W (2014). "Testing for association with multiple traits in generalized estimation equations, with application to neuroimaging data." NeuroImage 96, 309--325.