MSKAT: Multi-trait sequence kernel association test of variant set

In baolinwu/MSKAT: Various multi-trait variant-set association test methods

Description

Compute the variant set association test statistic and p-value

Usage

MSKAT(obj, G, W = NULL, W.beta = c(1, 25))

Arguments

obj	fitted null model from MSKAT.cnull
G	genotype matrix with SNPs in column
W	variant weight; use Beta dist weight if NULL
W.beta	Beta distribution parameters for the variant weight

Value

p.value

p-values for the two kernel statistics (Q and Q'; see ref)

Q

test statistics (Q and Q'; see ref)

References

Wu,B. and Pankow,J.S. (2016) Sequence kernel association test of multiple continuous phenotypes. Genetic Epidemiology, 40(2), 91-100.

Examples

Y = matrix(rnorm(2000), 1000,2)
X = matrix(rnorm(2000), 1000,2)
G = matrix(rbinom(10000,2,0.02), 1000,10)
MSKAT(MSKAT.cnull(Y,X), G, W.beta=c(1,25))
## time-consuming; not run
## X.list = vector('list',2); for(i in 1:2) X.list[[i]] = rbind(1, t(X))
## MKMR(t(Y),X.list, Gm=G, W.beta=c(1,25))

baolinwu/MSKAT documentation built on May 28, 2019, 6:37 p.m.