Description Usage Arguments Value Examples
Composite kernel association test for SNP-set analysis in pharmacogenetics (PGx) studies.
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G |
- genotype matrix. |
Tr |
- treatment vector, 0 indicates placebo, 1 indicates treatment. |
X |
- non-genetic covariates data matrix. |
y |
- response vector. Currently continuous and binary responses are supported. Survival response will be added soon. |
trait |
- response indicator. trait = "continuous" or "binary". |
ker |
- kernel. ker = "linear", "IBS", "Inter" (interaction kernel) and "RBF" (radial basis function kernel). |
grids |
- grids of the candidate weights. |
n_a |
- the number of intervals for manual integration (when integrate function fails). Default n_a = 1000. |
method |
- method for getting density of A (see details in the reference). Default method is Liu's method. |
subdiv |
- parameter of Davies' method. Default value is 1E6. |
pvals - p-values of each individual association test.
finalp - final p-value of the CKAT test.
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