MultiSTAAR (Multi-trait variant-Set Test for Association using Annotation infoRmation)

This is an R package for performing MultiSTAAR procedure in whole-genome sequencing studies.

Description

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.

Workflow Overview

Prerequisites

<a href="https://www.r-project.org">R</a> (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 <a href="https://software.intel.com/en-us/articles/using-intel-mkl-with-r">instructions</a> on building R with Intel MKL.

Dependencies

MultiSTAAR links to R packages <a href="https://cran.r-project.org/web/packages/Rcpp/index.html">Rcpp</a>, <a href="https://cran.r-project.org/web/packages/RcppArmadillo/index.html">RcppArmadillo</a> and <a href="https://github.com/xihaoli/STAAR">STAAR</a>, and also imports R packages <a href="https://cran.r-project.org/web/packages/Rcpp/index.html">Rcpp</a>, <a href="https://cran.r-project.org/web/packages/GMMAT/index.html">GMMAT</a>, <a href="https://bioconductor.org/packages/release/bioc/html/GENESIS.html">GENESIS</a>, <a href="https://github.com/xihaoli/STAAR">STAAR</a>, <a href="https://cran.r-project.org/web/packages/Matrix/index.html">Matrix</a>. These dependencies should be installed before installing MultiSTAAR.

Installation

library(devtools)
devtools::install_github("xihaoli/MultiSTAAR",ref="main")

Docker Image

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

Usage

Please see the <a href="docs/MultiSTAAR_manual.pdf">MultiSTAAR user manual</a> for detailed usage of MultiSTAAR package. Please see the <a href="https://htmlpreview.github.io/?https://github.com/xihaoli/MultiSTAAR/blob/master/docs/MultiSTAAR_vignette.html">MultiSTAAR tutorial</a> for an example of analyzing sequencing data using MultiSTAAR procedure. Please see the <a href="https://github.com/xihaoli/STAARpipeline-Tutorial">STAARpipeline tutorial</a> for a detailed example of analyzing sequencing data using MultiSTAAR.

Data Availability

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.

Version

The current version is 0.9.7.1 (November 14, 2024).

License

This software is licensed under GPLv3.

GNU General Public License, GPLv3