linkRARE: linkRARE

Description Usage Arguments Value Warning Author(s) References

View source: R/linkRARE.R

Description

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

Usage

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

Arguments

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.

Value

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

Warning

library(SKAT) is needed to run this function.

Author(s)

Sharon Lutz, Annie Thwing

References

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/linkRare documentation built on June 3, 2018, 6:37 p.m.