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.
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