MKMR: Multivariate Kernel Machine Regression test of rare variant...

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

Description

Return the variant set association test statistic and p-value. Aadapted from Maity et. al approach for rare variant set association test using weighted linear kernel.

Usage

MKMR(Y, X.list, Sigma = NULL, Gm, W = NULL, W.beta = c(1, 25),
  n.sim = NULL)

Arguments

Y	pxn matrix, each row is one response, each column is one subject
X.list	a list where each item of list is a qxn matricx (parametric design matrix), where each row is one covariate (possiblly different for all items in Y), intercept must be included!
Sigma	covariance matrix of multivariate outcomes; estimate from data if NULL
Gm	genotype matrix with SNPs in column
W	variant weight; use Beta dist weight if NULL
W.beta	Beta distribution parameters for the variant weight. Default to Beta(1,25).
n.sim	number of simulation to obtain the null distribution of the test statistic; using analytical method if NULL

References

Maity,A., Sullivan,P.F., Tzeng,J. (2012) Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regression. Genet. Epidemiol. 36, 686–695.

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