globalGSA-package: Gene-set analysis for combining p-values in a joint test of...
In globalGSA: Global Gene-Set Analysis for Association Studies.

Description Details Author(s) References

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.

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

Natalia Vilor, M.Luz Calle

Maintainer: natalia.vilor@uvic.cat

[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.

globalGSA documentation built on May 1, 2019, 9:19 p.m.