qb.model {qtlbim} | R Documentation

## Set up interacting QTL model for qb.mcmc

### Description

This function sets up a genome-wide interacting QTL model by specifying global constraints on models and priors on unknowns.

### Usage

    qb.model(cross, epistasis = TRUE, main.nqtl = 3,
      mean.nqtl = main.nqtl + 3, max.nqtl = NULL, interval = NULL,
      chr.nqtl = NULL,intcov = c(0), depen = FALSE,
      prop = c(0.5, 0.1, 0.05), ...)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`epistasis` | indicates if epistasis is included in the model: TRUE or FALSE
`main.nqtl` | prior expected number of main effect QTLs.
`mean.nqtl` | prior expected number for all QTLs on all chromosomes including QTLs with main effects, epistatic effects and gene-environment interactions.
`max.nqtl` | maximum number of QTLs allowed in the model. Default is l+3sqrt{l} where l is `main.qtl` for non-epistatic model and `mean.qtl` for epistatic model.
`interval` | minimum distance between any two flanking QTLs for all chromosomes. Default is the average distance between markers in each chromosome.
`chr.nqtl` | list of the maximum number of QTLs allowed to be detected on each chromosome. Default is the length of the chromosome divided by `interval`.
`intcov` | list of the fixed covariates with which gene-environment interaction will be considered.
`depen` | =TRUE will use dependent prior for indicator variables of epistatic effects.
`prop` | prior inclusion probabilities for epistatic effects in three different scenarios: when none,one and both the main effects of the two interacting QTL are included in the model. Note that the sum of the probabilities need not be equal to 1 and `prop` should be specified only when `depen=TRUE`.
`...` | Not used.

### Details

This function defines the model for Bayesian QTL mapping using `qb.mcmc`. This model considers two-way interaction as the highest level of both gene-gene and gene-environment interactions.

### Value

`qtl_envi` | Indicates if there is an interaction between the QTLs and environmental variables: TRUE or FALSE.

### Note

This function returns a list and hence should have a differenct name from that of the `cross` object.

### Author(s)

Dr. Nengjun Yi, et al., nyi@ms.ssg.uab.edu

### References

http://www.qtlbim.org

### See Also

`qb.data`, `qb.genoprob`, `qb.mcmc`

### Examples

    qbModel <- qb.model(cross, chr.nqtl = rep(3,nchr(cross)), intcov = 1,
      interval = rep(10,3))

[Package qtlbim version 1.6.5 Index]