SKATOL: Optimal sequence kernel association test (SKAT-O) for binary...
In baolinwu/mkatr: Miscellaneous variant-set association test methods

Description Usage Arguments Value References Examples

Compute the significance p-value for SKAT-O based on LRT. The computational algorithm is based on a new approach described in detail at Wu et. al (2015).

1	SKATOL(obj, G, W.beta, rho = c(0, 0.1^2, 0.2^2, 0.3^2, 0.4^2, 0.5^2, 0.5, 1))

`obj`	a fitted null binomial model using KAT.null()
`G`	genotype matrix, sample in rows, variant in columns
`W.beta`	Beta parameters for variant weights
`rho`	weights for burden test

SKATOL p-value

Lee, S., Wu, M. C., and Lin, X. (2012) Optimal tests for rare variant effects in sequencing association studies. Biostatistics, 13, 762-775.

Wu, M.C., Lee, S., Cai, T., Li, Y., Boehnke, M., and Lin, X. (2011) Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). American Journal of Human Genetics, 89, 82-93.

Wu,B., Pankow,J.S., Guan,W. (2015) Sequence kernel association analysis of rare variant set based on the marginal regression model for binary traits. Genetic Epidemiology, 39(6), 399-405.

Wu,B., Guan,W., Pankow,J.S. (2016) On efficient and accurate calculation of significance p-values for sequence kernel association test of variant set. Annals of human genetics, 80(2), 123-135.

library(CompQuadForm)
D = rbinom(5000,1,0.5); X = matrix(rnorm(10000),5000,2)
G = matrix(rbinom(100000,2,0.01), 5000,10)
SKATL(KAT.null(D,X), G, c(1.5,25.5))
SKATOL(KAT.null(D,X), G, c(1.5,25.5))
## library(SKAT)
## SKAT(G, SKAT_Null_Model(D~X, out_type='D'), method='davies')$p.value
## SKAT(G, SKAT_Null_Model(D~X, out_type='D'), method='optimal.adj')$p.value