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

In PIGE: Self Contained Gene Set Analysis for Gene- And Pathway-Environment Interaction Analysis

Description

An R package for computing gene and pathway p-values using the Adaptive Rank Truncated test (ARTP). This package can be used to analyze pathways/genes based on a genetic association study, with a binary case-control outcome or a survival outcome. This package is an extension of the ARTP method developped by Kai Yu (Genet Epidemiol. 2009) for gene- and pathway-environment interaction analysis.

Details

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. The function ARTP.GE 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.GE could be obtained by calling the function permutation.snp and the function compute.p.snp.obs.

Author(s)

Benoit Liquet [e-mail]
Therese Truong [e-mail]

References

Yu K, Li Q, Berger AW, Pfeiffer R, Rosenberg P, Caporaso N, Kraft P, Chatterjee N (2009). Pathway analysis by adaptive combination of P-values. Genet Epidemiol 33:700-709.

See Also

ARTP.GE, permutation.snp, compute.p.snp.obs

PIGE documentation built on May 1, 2019, 11:30 p.m.