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]