ARTP2 is an R package of biological pathway analysis or pathway meta-analysis for genome-wide association studies (GWAS). It also provides tools for gene-level test as a special case. ARTP2 is an enhanced version of two previously released packages ARTP and AdaJoint. The current version is 0.9.20.
Features
- Association test on user-defined genes or pathways
- No need to assume independence between genes in a pathway (genes can be closeby or overlapped)
- Accepting individual-level genetic data or SNP-level summary statistics from one or multiple GWAS
- Supporting continuous or binary outcome (case-control studies)
- Comprehensive data pre-processing options
- Automatic allele validation and matching in processing inputs from summary data
- Inflation factor adjustment
- Toolkit for SNP-level meta-analysis
- Parallelization under Linux-like OS using OpenMP
Download Software:
- License Agreement
- Package source: ARTP2_0.9.28.tar.gz
- Windows binary: ARTP2_0.9.28.zip
- OS X binary: ARTP2_0.9.28.tgz
Note: While this page is updated frequently, the GitHub page, accessible through CRAN, is updated most frequently.
References:
- Zhang H, Wheeler W, Shi J, Hyland P, Yang Y, Chatterjee N, Yu K. Pubmed Abstract: A powerful procedure for pathway meta-analysis using summary statistics identifies multiple pathways associated with type 2 diabetes. PLOS Genet 2016.
- Zhang H, Shi J, Liang F, Wheeler W, Stolzenberg-Solomon R, Yu K. Pubmed Abstract: A fast multilocus test with adaptive SNP selection for large-scale genetic association studies. Eur J Human Genet 2014.
- Yu K, Li Q, Bergen AW, Pfeiffer RM, Rosenberg PS, Caporaso N, Kraft P, Chatterjee N. Pubmed Abstract: Pathway analysis by adaptive combination of p-values. Genet Epidemiol 2009.
Notes
ARTP version 1 and AdaJoint are no longer being maintained. For access to those files, please email Kai Yu.