Adaptive Rank Truncated Product - Version 2 (ARTP2)

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
• Download from CRAN

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.