genMOSS: Functions for the Bayesian analysis of GWAS data

Description Details Author(s) References Examples

Description

The genMOSS package implements the Mode Oriented Stochastic Search (MOSS) of Dobra and Massam (2010) as well as a simple moving window approach (see Sun et. al (2006) and Wu et. al (2010)) to identify combinations of SNPs that are associated with a response.

Details

Package: genMOSS
Type: Package
Version: 1.2
Date: 2014-12-01
License: GPL-2
LazyLoad: yes

The function MOSS_GWAS implements the MOSS algorithm while the mWindow implements the moving window approach.

Author(s)

Authors: Matthew Friedlander, Adrian Dobra, Helene Massam, and Laurent Briollais, Maintainer: Matthew Friedlander <friedlander.matthew@gmail.com>

References

[1] Massam, H., Liu, J. and Dobra, A. (2009). A conjugate prior for discrete hierarchical log-linear models. Annals of Statistics, 37, 3431-3467.

[2] Dobra, A., Briollais, L., Jarjanazi, H., Ozcelik, H. and Massam, H. (2010). Applications of the mode oriented stochastic search (MOSS) algorithm for discrete multi-way data to genomewide studies. Bayesian Modeling in Bioinformatics, Taylor & Francis (Dey, D., Ghosh, S., and Mallick, B., eds.), 63-93.

[3] Dobra, A. and Massam, H. (2010). The mode oriented stochastic search (MOSS) algorithm for log-linear models with conjugate priors. Statistical Methodology, 7, 240-253.

[4] Sun, J., Levin, A., Boerwinkle, E., Robertson, H., and Kardia, S. (2006). A scan statistic for identifying chromosomal patterns of SNP association. Genetic Epidemiology, 30, 627-635.

[5] Wu, M., Kraft, P., Epstein, M., Taylor, D., Chanock, S., Hunter, D., and Lin, X. (2010). Powerful SNP-set analysis for case-control genome-wide association studies. The American Journal of Human Genetics, 86, 929-942.

Examples

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data(simuCC)
data <- simuCC[,c(1002,2971,rep(5978:6001))]
# The SNPs in columns 1002 and 2971 of simuCC called rs4491689 and rs6869003 cause the disease.
set.seed(7)
MOSS_GWAS (alpha = 1, c = 0.1, cPrime = 0.0001, q = 0.1, replicates = 1, 
           maxVars = 3, data, dimens = c(rep(3,25),2), confVars = NULL, k = NULL)
s <- mWindow (data, dimens = c(rep(3,25),2), alpha = 1, windowSize = 2)
head (s, n = 5)

genMOSS documentation built on May 2, 2019, 2:31 p.m.