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globalGSA (version 1.0)

globalGSA-package: Gene-set analysis for combining p-values in a joint test of association between a phenotype and a set of genetic variants (SNPs). Previously, a global test for the best inheritance model of each SNP is performed.

Description

This package implements three different Gene-set analysis (GSA) methods for combining individual p-values of a set of SNPs. Each method provides a p-value for a joint test of association between the phenotype and the specified set of genetic variants. The three implemented methods are: Fisher method [1], Simes method [2] and ARTP method [3].

Since the SNPs in a set may follow different modes of inheritance, previously to the GSA, a global test for the best inheritance model (dominant, recessive, log-additive and co-dominant) is performed on every SNP. The permutational p-value of the best model is obtained.

Arguments

Details

Package:
globalGSA
Type:
Package
Version:
1.0
Date:
2013-09-22
License:
GPL (>= 2)

References

[1] Fisher, R.A. (1925). Statistical Methods for Research Workers. ISBN 0-05-002170-2.

[2] Simes, R.J. (1986). An Improved Bonferroni Procedure for Multiple Tests of Significance. Biometrika, 73, 751-754.

[3] Yu, K. Li, Q. Bergen, A.W. Pfeiffer, R.M. Rosenberg, P.S. Caporaso, N. Kraft, P. and Chatterjee,N. (2009). Pathway analysis by adaptive combination of P-values. Genet, Epidemiol. December; 33(8): 700-709.