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.

ARTP2 has an online version accepting inputs from summary statistics of GWAS.

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:

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, June 30.
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 May; Epub 2013 Sep 11.
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, Dec.

Notes

ARTP version 1 and AdaJoint are no longer being maintained. For access to those files, please email Han Zhang or Kai Yu.