linkRARE: linkRARE
In SharonLutz/linkBayes: This package runs the linkRARE function

Description Usage Arguments Value Warning Author(s) References

View source: R/linkRARE.R

This function incorporates linkage data in genetic association studies with 2 approaches: 1) Bayesian Hierarchical model and 2) frequentist approach for rare variants.

1	linkRARE(x, y, npl, z = NULL, SEED = 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)

SharonLutz/linkBayes documentation built on May 17, 2019, 10:40 a.m.