SKATT: Sequence kernel association test (SKAT) for quantitative...
In baolinwu/mkatr: Miscellaneous variant-set association test methods

Description Usage Arguments Value References

Compute the significance p-value for SKAT based on marginal Wald-statistics

1	SKATT(obj, G, W.beta = c(1.25, 25.5))

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

SKAT p-value

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, M. C., Kraft, P., Epstein, M. P.,Taylor, D., M., Chanock, S. J., Hunter, D., J., and Lin, X. (2010) Powerful SNP Set Analysis for Case-Control Genome-wide Association Studies. American Journal of Human Genetics, 86, 929-942.

Duchesne, P. and Lafaye De Micheaux, P. (2010) Computing the distribution of quadratic forms: Further comparisons between the Liu-Tang-Zhang approximation and exact methods, Computational Statistics and Data Analysis, 54, 858-862.

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.

baolinwu/mkatr documentation built on May 14, 2019, 6:03 a.m.