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.
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.
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.