bim.effects {bim} | R Documentation |
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 |
add.sd |
SD for additive effect |
dom |
dominance effect (if present) |
dom.sd |
SD for dominance effect |
Brian S. Yandell, yandell@stat.wisc.edu
http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl
data( vern ) data( verngeo.bim ) vern.qtl <- bim.effects( verngeo.bim, vern, 2 ) plot.bim.effects( verngeo.bim, vern, 2, qtl = vern.qtl )