bim.effects {bim}R Documentation

Bayesian QTL map of loci and effects


Histogram of QTL loci plus scatter plots and smooth estimates of QTL effects (additive and dominance–Mather-Jinks model).


plot.bim.effects(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
  chr, bw = 2, qtl = <<see below>>, cex, level = .80,
  project=<<see below>>, main=<<see below>>, mfcol=<<see below>>, ... )
bim.effects(x, cross, nqtl = 1, pattern = NULL, exact = FALSE, chr,
  bw = 2, qtl = <<see below>>)


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
qtl QTL estimate information (see value)
cex character expansion for scatter plots
prefix prefix for chromosome names, typically c
level level for HPD region from seq(.5,.95,by=.05)
project project identifier, default is name of x argument
main title, with default expression(project summaries with m >= nqtl) and substitutions for project and nqtl
mfcol parameter to par set to 2 or 3 depending on if dominance is present
... graphical parameters can be given as arguments to plot


Model averaging conditional on at least nqtl and at least chromosome pattern QTL in model. bim.effects uses bim.qtl to estimate the QTL First row has histogram of loci overlaid with smoothed density estimate (blue line) and HPD regions (red circles along origin). Second row is additive effect; third if present has dominance effect. Smoothing spline fit along scatter plot to estimate mean effects (solid blue line), plus or minus two SDs (dashed blue line; estimated as well by smoothing spline). Simple linear regression used if 50 or fewer samples for a chromosome. Purple triangles indicate marker locations if supplied. Red circles and vertical dashed lines at estimated loci and effects. Vertical black lines delineate chromosomes.


bim.effects returns an enhanced version of the bim.qtl object, with additional elements

add additive smoothing spline by chromosome
dom dominance smoothing spline by chromosome (if present)
est estimates of QTL
chrom chromosome name
loci loci position along chromosome
add additive effect SD for additive effect
dom dominance effect (if present) SD for dominance effect


Brian S. Yandell,


See Also



data( vern )
data( verngeo.bim )

vern.qtl <- bim.effects( verngeo.bim, vern, 2 )
plot.bim.effects( verngeo.bim, vern, 2, qtl = vern.qtl )

[Package bim version 1.01-1 Index]