gamut: GAMuT: Gene Association with Multiple Traits
In baolinwu/MSKAT: Various multi-trait variant-set association test methods

Description Usage Arguments Value References

Return the multi-trait variant set association test p-values from the Broadaway et. al (2016) approach. Both tests from linear kernel and projection matrix are computed.

1	gamut(PHENO, GENO, COVAR = NULL, W = NULL, W.beta = c(1, 25))

`PHENO`	outcome matrix. sample in rows.
`GENO`	genotype matrix. sample in rows.
`COVAR`	covariate matrix to be adjusted. sample in rows.
`W`	variant weight; use Beta dist weight if NULL
`W.beta`	Beta distribution parameters for the variant weight. Default to Beta(1,25).

a p-value vector p.value with two components

proj: p-value for GAMuT with the projection matrix kernel
linear: p-value for GAMuT with the linear kernel

Broadaway, K.A., Cutler, D.J., Duncan, R., Moore, J.L., Ware, E.B., Jhun, M.A., Bielak, L.F., Zhao, W., Smith, J.A., Peyser, P.A., Kardia, S.L.R., Ghosh, D., Epstein, M.P. (2016). A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants. The American Journal of Human Genetics, 98, 525–540.

Original R codes posted at http://genetics.emory.edu/labs/epstein/software/gamut

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