BayesAB: Estimte SNP Effects by MCMC - Bayes (A and B) - beta
In gdmp: Genomic Data Management

Description Usage Arguments Details Value References See Also

View source: R/BayesAB.R

BayesAB is an implementation of Bayes A and B for estimating direct SNP effects in high dimensional data problems (p >> N). BayesAB utilizes the C Function cBaysABF for speed ..

1	BayesAB(ga, numiter = 5000, numMHIter = 10, Pi = .9, y)

`ga`	A matrix of genotypes with a number of rows identical to the number of genotyped individuals and a number of columns identical to the number of SNPs. Values in the matrix are 0, 1, 2, & 5 for homozygous, heterozygous, other homozygous, & unknown genotypes, respectively.
`numiter`	Number of iterations
`numMHIter`	Number of Metropolis-Hastings iterations. Set to a value of 1 with Bayes A.
`Pi`	Proportion of SNP loci with 0 effect. Set to 0 to run Bayes A instead of B.
`y`	Trait phenotypes or conventional breeding values

This function runs Bayes A and B to estimate direct SNP effects based on a matrix of genotypes, ga and a vector of adjusted phenotypes, y, (Meuwissen et al., 2001; Genetics 157:1819-1829). This is essential in high dimensional data problems with highly overparameterized models (p >> N). To run Bayes A, set Pi to 0 and numMHIter to 1.

Other data management functions in gdmp can be used to construct the integer matrix of genotypes, ga, to use as input to BayesAB.

A list object with a vector of SNP estimates, meanb, and a vector of genomic values for individuals, aHat, are returned. It is also possible to extract the number of SNP loci in nLoci.

Meuwissen et al. (2001). Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics, 157, 1819–1829.

BayesCpi

gdmp documentation built on May 1, 2019, 8:07 p.m.