This is an R package for performing MultiSTAAR procedure in whole-genome sequencing studies.
MultiSTAAR is an R package for performing Multi-trait variant-Set Test for Association using Annotation infoRmation (MultiSTAAR) procedure in whole-genome sequencing (WGS) studies. MultiSTAAR is a general framework that (1) leverages the correlation structure between multiple phenotypes to improve power of multi-trait analysis over single-trait analysis, and (2) incorporates both qualitative functional categories and quantitative complementary functional annotations using an omnibus multi-dimensional weighting scheme. MultiSTAAR accounts for population structure and relatedness, and is scalable for jointly analyzing large WGS studies of multiple correlated traits.
R (recommended version >= 3.5.1)
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.
MultiSTAAR links to R packages Rcpp, RcppArmadillo and STAAR, and also imports R packages Rcpp, GMMAT, GENESIS, STAAR, Matrix. These dependencies should be installed before installing MultiSTAAR.
library(devtools)
devtools::install_github("xihaoli/MultiSTAAR",ref="main")
A docker image for MultiSTAAR, including R (version 3.6.1) built with Intel MKL and all STAAR-related packages (STAAR, MultiSTAAR, SCANG, STAARpipeline, STAARpipelineSummary) pre-installed, is located in the Docker Hub. The docker image can be pulled using
docker pull zilinli/staarpipeline:0.9.7
Please see the MultiSTAAR user manual for detailed usage of MultiSTAAR package. Please see the STAARpipeline tutorial for a detailed example of analyzing sequencing data using MultiSTAAR.
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 0.9.7 (October 30, 2023).
This software is licensed under GPLv3.
