R: The SPU and aSPU tests for multiple traits - single SNP...
GEEaSPU
R Documentation
The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.
Description
It gives p-values of the GEESPU tests and GEEaSPU test.
Usage
GEEaSPU(traits, geno, Z = NULL, model = c("binomial", "gaussian"),
gamma = c(1:8, Inf), n.sim = 1000, corstr = "independence")
Arguments
traits
trait matrix. The row for individuals and the column for traits.
geno
A matrix of genetic information.
Z
covariates.
model
Use "gaussian" for a quantitative trait, and use "binomial" for a binary trait.
gamma
power used in GEEaSPU test. A vector of the powers.
n.sim
number of simulations.
corstr
a character string specifying the correlation structure. The following are permitted: "independence", "fixed", "stat_M_dep", "non_stat_M_dep", "exchangeable", "AR-M" and "unstructured"
Value
p-values for the GEE-SPU and GEE-aSPU test.
Author(s)
Junghi Kim, Wei Pan and Il-Youp Kwak
References
Yiwei Zhang, Zhiyuan Xu, Xiaotong Shen, Wei Pan (2014)
Testing for association with multiple traits in generalized estimation equations, with application to neuroimaging data.
Neuroimage. 96:309-25
Examples
traits <- matrix(rnorm(100*5, 0,1), ncol=5)
Z <- rnorm(100, 2, 0.5)
geno <- rbinom(100, 2, 0.5)
out <- GEEaSPU(traits, geno, Z = NULL, model = "gaussian",
gamma = c(1:8,Inf), n.sim = 100)