Description Usage Arguments Details Value References
Efficient SKAT-O p-value calculation using marginal variant score statistics directly
1 2 |
obj |
a fitted null model using KAT.null() or KAT.cnull() |
G |
genotype matrix, sample in rows, variant in columns |
W.beta |
Beta parameters for variant weights |
rho |
proportion weight assigned to burden test statistic |
Efficiently compute the SKAT-O significance p-value based on the variant test statistics (typically of much smaller dimension). The individual p-values of weighted SKAT and burden test are comptued more accurately using the SKATh. To obtain more accruate results, the one-dimensional integration is computed based on the convolution of survival function of 1-DF chi-square mixtures and 1-DF chi-square density function. For details, please see the Wu et. al (2016) reference.
SKAT-O 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,B., Guan,W., and Pankow,J.S. (2016) On efficient and accurate calculation of significance p-values for sequence kernel association test of variant set. AHG, 80(2), 123-135.
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