Description Usage Arguments Details Value References See Also

`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.

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