SurvSTAAR is an R package for performing variant-Set Test for Association using Annotation infoRmation (STAAR) procedure in whole-genome sequencing (WGS) studies in time-to-event traits. SurvSTAAR is a general framework that incorporates both qualitative functional categories and quantitative complementary functional annotations using an omnibus test SurvSTAAR-O. SurvSTAAR accounts for population structure and sample relatedness, and addresses challenges posed by heavily censored phenotypes and low-frequency variants.
R (recommended version >= 4.0.0)
For optimal computational performance, it is recommended to use an R version configured with the Intel Math Kernel Library (or other fast BLAS/LAPACK libraries). See the instructions on building R with Intel MKL.
SurvSTAAR imports R packages survival, Matrix, data.table, and CompQuadForm. These dependencies should be installed before installing SurvSTAAR.
library(devtools)
devtools::install_github("Cui-yd/SurvSTAAR")
Please see the SurvSTAAR examples using a toy data for example analyses of sequencing data using the SurvSTAAR procedure. Please see the SurvSTAARpipeline for scripts to analyze sequencing data using SurvSTAAR on a High Performance Cluster or the UK Biobank Research Analysis Platform.
The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the Functional Annotation of Variant - Online Resource (FAVOR) site and FAVOR Essential Database.
The current version is 0.1.0 (February 20, 2025).
This software is licensed under GPLv3.
