Description Usage Arguments Value Warning Author(s) References
This function incorporates linkage data in genetic association studies with 2 approaches: 1) Bayesian Hierarchical model and 2) frequentist approach for rare variants.
1 |
x |
is a matrix of rare variants in the region. |
y |
is the outcome for case-control status. y=1 for case and y=0 for control. |
npl |
is the NPL score. |
z |
is the matrix (or vector) of covariates, default is NULL. |
SEED |
sets the seed for SKAT. Default is 1. |
p-value |
The significance from SKAT with all subjects, and the significance from SKAT excluding subjects with NPL<0 |
rare variants |
The number of rare variants from all subjects, and the number of rare variants excluding subjects with NPL<0 |
library(SKAT) is needed to run this function.
Sharon Lutz, Annie Thwing
Lutz SM, Pelijto A, Thwing A, Zhang W, Fingerlin TE (2017) A Bayesian Approach to Integrate Family-Specific Linkage Scores in Case-Control Tests of Association. Genetic Epidemiology (Submitted)
Lutz SM, Pelijto A, Thwing A, Zhang W, Fingerlin TE (2017) An Approach to Integrate Family-Specific Linkage Scores in Case-Control Tests of Associations of Rare Variants. BMC Genetics. (In preparation)
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