ARTP: Gene and pathway p-values using the Adaptive Rank Truncated...

In ARTP: Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product

Description

An R package for computing gene and pathway p-values using the Adaptive Rank Truncated test. This package can be used to analyze pathways/genes based on a genetic association study, with either a continuous or a binary case-control outcome.

Details

It is increasingly recognized that pathway analyses-a joint test of association between the outcome and a group of single nucleotide polymorphisms (SNPs) within a biological pathway-could potentially complement single-SNP analysis and provide additional insights for the genetic architecture of complex diseases. Building upon existing P-value combining methods, we propose a class of highly flexible pathway analysis approaches based on an adaptive rank truncated product statistic that can effectively combine evidence of associations over different SNPs and genes within a pathway. The statistical significance of the pathway-level test statistics is evaluated using a highly efficient permutation algorithm that remains computationally feasible irrespective of the size of the pathway and complexity of the underlying test statistics for summarizing SNP- and gene-level associations. We demonstrate through simulation studies that a gene-based analysis that treats the underlying genes, as opposed to the underlying SNPs, as the basic units for hypothesis testing, is a very robust and powerful approach to pathway-based association testing.

The function ARTP_pathway is used to compute gene and pathway p-values provided that the observed and permutation p-values for each SNP already exist in files. The input files required for ARTP_pathway can be obtained by calling the function runPermutations.

Author(s)

Kai Yu <[e-mail]> and William Wheeler <[e-mail]>

References

Yu K, Li Q, Bergen AW, Pfeiffer RM, Rosenberg PS, Caporaso N, Kraft P, Chatterjee N Pathway analysis by adaptive combination of P-values Genet Epidemiol 33(8):700-9; 2009 Dec.

ARTP documentation built on May 2, 2019, 6:51 a.m.