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Discovering the causes of cancer and the means of prevention

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. A powerful procedure for pathway meta-analysis using summary statistics identifies multiple pathways associated with type 2 diabetes.
  • Zhang H, Shi J, Liang F, Wheeler W, Stolzenberg-Solomon R, Yu K. (2014) A fast multilocus test with adaptive SNP selection for large-scale genetic association studies. European Journal of Human Genetics, 22, 696 - 702.
  • Yu K, Li Q, Bergen AW, Pfeiffer RM, Rosenberg PS, Caporaso N, Kraft P, Chatterjee N. (2009) Pathway analysis by adaptive combination of p-values. Genetic Epidemiology, 33(8), 700 - 709.

Notes

ARTP version 1 and AdaJoint are no longer being maintained.  For access to those files, please email Han Zhang or  Kai Yuif you need access to the old files.