bim. {bim} | R Documentation |
Smooth density, point estimates and HPD regions for QTL loci. Loci are estimated at peaks of density.
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, level = 0.80, col = "black", add = FALSE, ...)
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 |
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.
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}
Brian S. Yandell, yandell@stat.wisc.edu
http://www.stat.wisc.edu/~yandell/qtl/software/bmqtl
data( vern ) data( verngeo.bim ) plot.bim.qtl( verngeo.bim, vern, 2 )