The "gskat" Package

This package implements a family based association test via GEE Kernel Machine (SKAT) score test. It has functions to test an association between SNP/SNV sets and binary/continuous phenotypes.

References:

Wang X. et al. GEE-Based SNP Set Association Test for Continuous and Discrete Traits in Family-Based Association Studies. Genetic Epidemiology (2013) 37: 778-786

Wang X. et al. Rare variant association test in family based sequencing studies. Breifings in Bioinformatics (2016+, To appear online soon).

Installation Instructions

Start R and then install the 'gskat' package with the following commands.

#install.packages("devtools")
library(devtools)
install_github("gskat",username="xfwang")

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zhang.zhenyu@stonybrook.edu

xuefeng.wang@stonybrook.edu

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Q&A: Gskat now have function for testing without any covariates. A new function called gskat_seq_opt2 has just been added for testing without covaraites.

Does gskat provides a function to do null model fitting to speed up the large scale test? We are working on this in the new package.

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Updates: