ASPBay (version 1.2)

ASP.Bayesian: Samples in the posterior distribution of the frequencies and OR

Description

Samples using Metropolis-Hasting Algorithm in the posterior distribution of the four haplotype frequencies and OR

Usage

ASP.Bayesian(N, Tem_Gen, Index_Gen, IBD, snp, thin = 1, sd.freq = 0.05,
                     sd.psi = 0.05, p0 = c(rep(1/4, 4), 1), psi.prior = 0)

Arguments

N

Number of Metropolis-Hastings iterations

Tem_Gen

Genotypes of controls (denoted by the number of alternative allele)

Index_Gen

Genotypes of index cases

IBD

IBD states for each affected sib-pair

snp

Names or number column of the SNP to consider

thin

Thinning parameter (keep only every thin-th draw)

sd.freq

Random walk standard deviation of the frequency logarithms

sd.psi

Random walk standard deviation of the OR

p0

The initial point of random walk

psi.prior

Precision of gaussian log(OR) prior (0 = improper flat prior)

Value

• List of 5 vectors of length N/thin with components:
• f_ab
  Sample of the haplotype composed by the two alternative alleles
• f_Ab
  Sample of the haplotype composed by the reference allele for the causal (unobserved) locus and the alternative alleles for the observed locus
• f_aB
  Sample of the haplotype composed by the alternative allele for the causal (unobserved) locus and the reference alleles for the observed locus
• f_AB
  Sample of the haplotype composed by the two reference alleles
• OR
  Sample of the OR

Details

Samples using Metropolis-Hasting and likelihood defined by data. More precisely, give the frequency samples of haplotypes for observed SNP and unobserved causal SNP and give the sample of the odds ratio associated to the causal SNP.

References

Dandine-Roulland, Claire and Perdry, Herve. Where is the causal variant? On the advantage of the family design over the case-control design in genetic association studies. Submitted to Eur J Hum Genet

See Also

ASP.Selection, Graphs.Bayesian

Examples

data(ASPData)
B <- ASP.Bayesian(1e5, ASPData$Control, ASPData$Index,
                  ASPData$IBD, 15 )