bim. {bim}R Documentation

Bayesian QTL estimation and mapping of loci

Description

Smooth density, point estimates and HPD regions for QTL loci. Loci are estimated at peaks of density.

Usage

bim.qtl(x, cross, nqtl=1, pattern=NULL, exact=FALSE,
  chr, bw=2, levels = seq(.5,.95,by=.05) )
plot.bim.qtl(x, cross, nqtl = 1, pattern = NULL,
  exact = FALSE, chr, bw = 2, qtl=<<see below>>,
  level = 0.80, col = "black", add = FALSE, ...) 

Arguments

x object of class bim
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
chr subset of chromosomes to plot (numerical indices or chromosome names)
bw bandwidth for loci density
levels saved levels for HPD region
qtl QTL estimate information (see value)
level level for HPD region from seq(.5,.95,by=.05)
col line color
add create new plot if FALSE
... graphical parameters can be given as arguments to plot

Details

Model averaging conditional on at least nqtl QTL and at least chromosome pattern in model. bim.qtl does estimation of density and loci as well as high probability density (HPD) region. plot.bim.qtl calls bim.qtl and plots the density curve. See plot.bim.effects for enhanced plots with HPD and effects estimates.

Value

bim.qtl returns (and plot.bim.qtl silently returns) a list containing:

loci data frame with chr = chromosome name, x = locus on chromosome, y = height of density
dens list of density objects by chromosome
hpd

{density critical values for high probability density (HPD) region}

Author(s)

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

References

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

See Also

plot.bim.effects

Examples

data( vern )
data( verngeo.bim )

plot.bim.qtl( verngeo.bim, vern, 2 )

[Package bim version 1.01-1 Index]