plot.bim.model {bim} | R Documentation |

## Graphical model assessment for Bayesian interval mapping

### Description

Model-averaged posteriors and posterior/prior ratios for graphical Bayes
factor assessment. First row concerns number of QTL, second row
evaluates pattern of QTL across chromosomes.

### Usage

plot.bim.model( x, cross = NULL, nqtl = 1, pattern=NULL, exact=FALSE,
cutoff = 1, assess = <<see below>>, ... )

### Arguments

`x` |
object of class `bim` or class `bim.model` |

`cross` |
corresponding object of class `cross` |

`nqtl` |
subset on number of QTL |

`pattern` |
subset on chromosome pattern of QTL |

`exact` |
subset on exact pattern or number of QTL if true |

`cutoff` |
percent cutoff for inclusion in model selection |

`assess` |
object of class `bim.model` from `bim.model` |

`...` |
graphical parameters can be given as arguments to
`plot` |

### Details

`plot.bim.model`

uses results (`assess`

) of `bim.model`

and arranges plots on a single page. If `x`

is of class
`bim.model`

, then `assess`

is set to its value and the other
arguments are ignored. Left plot is of posterior against model
identifier, while right plot assesses Bayes factors. Since Bayes
factors are ratios of `posterior/prior`

ratios, a semi-log plot
of `posterior/prior`

against model identifier (*m* = number
of QTL or *M* = model pattern) provides a graphical model
assessment tool with a BF threshold yardstick.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

### See Also

`bim.model`

### Examples

data( vern )
data( verngeo.bim )
plot.bim.model( verngeo.bim, vern, 2 )

[Package

*bim* version 1.01-1

Index]