This is an R package for performing phenome-wide association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline.
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.
STAARpipelinePheWAS imports R packages STAAR, MultiSTAAR, STAARpipeline, dplyr, SeqArray, SeqVarTools, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, Matrix. These dependencies should be installed before installing STAARpipelinePheWAS.
library(devtools)
devtools::install_github("li-lab-genetics/STAARpipelinePheWAS",ref="main")
Please see the STAARpipelinePheWAS user manual for detailed usage of STAARpipelinePheWAS package.
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 0.9.7.1 (April 23, 2025).
If you use STAARpipelinePheWAS for your work, please cite:
Zilin Li*, Xihao Li*, Hufeng Zhou, Sheila M. Gaynor, Margaret Sunitha Selvaraj, Theodore Arapoglou, Corbin Quick, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K. Arnett, Paul L. Auer, Lawrence F. Bielak, Joshua C. Bis, Thomas W. Blackwell, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jennifer A. Brody, Brian E. Cade, Matthew P. Conomos, Adolfo Correa, L. Adrienne Cupples, Joanne E. Curran, Paul S. de Vries, Ravindranath Duggirala, Nora Franceschini, Barry I. Freedman, Harald H. H. Göring, Xiuqing Guo, Rita R. Kalyani, Charles Kooperberg, Brian G. Kral, Leslie A. Lange, Bridget M. Lin, Ani Manichaikul, Alisa K. Manning, Lisa W. Martin, Rasika A. Mathias, James B. Meigs, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Take Naseri, Jeffrey R. O’Connell, Nicholette D. Palmer, Patricia A. Peyser, Bruce M. Psaty, Laura M. Raffield, Susan Redline, Alexander P. Reiner, Muagututi’a Sefuiva Reupena, Kenneth M. Rice, Stephen S. Rich, Jennifer A. Smith, Kent D. Taylor, Margaret A. Taub, Ramachandran S. Vasan, Daniel E. Weeks, James G. Wilson, Lisa R. Yanek, Wei Zhao, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Jerome I. Rotter, Cristen J. Willer, Pradeep Natarajan, Gina M. Peloso, & Xihong Lin. (2022). A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19(12), 1599-1611. PMID: 36303018. PMCID: PMC10008172. DOI: 10.1038/s41592-022-01640-x.
Xihao Li*, Zilin Li*, Hufeng Zhou, Sheila M. Gaynor, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K. Arnett, Stella Aslibekyan, Christie M. Ballantyne, Lawrence F. Bielak, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jai G. Broome, Matthew P. Conomos, Adolfo Correa, L. Adrienne Cupples, Joanne E. Curran, Barry I. Freedman, Xiuqing Guo, George Hindy, Marguerite R. Irvin, Sharon L. R. Kardia, Sekar Kathiresan, Alyna T. Khan, Charles L. Kooperberg, Cathy C. Laurie, X. Shirley Liu, Michael C. Mahaney, Ani W. Manichaikul, Lisa W. Martin, Rasika A. Mathias, Stephen T. McGarvey, Braxton D. Mitchell, May E. Montasser, Jill E. Moore, Alanna C. Morrison, Jeffrey R. O'Connell, Nicholette D. Palmer, Akhil Pampana, Juan M. Peralta, Patricia A. Peyser, Bruce M. Psaty, Susan Redline, Kenneth M. Rice, Stephen S. Rich, Jennifer A. Smith, Hemant K. Tiwari, Michael Y. Tsai, Ramachandran S. Vasan, Fei Fei Wang, Daniel E. Weeks, Zhiping Weng, James G. Wilson, Lisa R. Yanek, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Benjamin M. Neale, Shamil R. Sunyaev, Gonçalo R. Abecasis, Jerome I. Rotter, Cristen J. Willer, Gina M. Peloso, Pradeep Natarajan, & Xihong Lin. (2020). Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics, 52(9), 969-983. PMID: 32839606. PMCID: PMC7483769. DOI: 10.1038/s41588-020-0676-4.
This software is licensed under GPLv3.
