plot.pxg {qtl}R Documentation

Plot phenotypes versus marker genotypes.

Description

Plot the phenotype values versus the genotypes at a marker or markers.

Usage

plot.pxg(x, marker, pheno.col=1, jitter=1, infer=TRUE,
         pch , ylab, main, ...)

Arguments

x An object of class cross. See read.cross for details.
marker Marker name (a character string; can be a vector).
pheno.col Column number in the phenotype matrix which should be used as the phenotype.
jitter A positive number indicating how much to spread out the points horizontally. (Larger numbers correspond to greater spread.)
infer If TRUE, missing genotypes are filled in with a single random imputation and plotted in red; if FALSE, only individuals typed at the specified marker are plotted.
pch Plot symbol.
ylab Label for y-axis.
main Main title for the plot. If missing, the names of the markers are used.
... Ignored at this point.

Details

Plots the phenotype data against the genotypes at the specified marker. If infer=TRUE, the genotypes of individuals that were not typed is inferred based the genotypes at linked markers via a single imputation from sim.geno; these points are plotted in red. For each genotype, the phenotypic mean is plotted, with error bars at +/- 1 SE.

Value

A data.frame with initial columns the marker genotypes, then the phenotype data, then a column indicating whether any of the marker genotypes were inferred (1=at least one genotype inferred, 0=none were inferred).

Author(s)

Karl W Broman, kbroman@jhsph.edu; Brian Yandell

See Also

find.marker, effectplot, find.flanking

Examples

data(listeria)
mname <- find.marker(listeria, 5, 28) # marker D5M357
plot.pxg(listeria, mname)

mname2 <- find.marker(listeria, 13, 26) # marker D13Mit147
plot.pxg(listeria, c(mname, mname2))

data(fake.f2)
mname <- find.marker(fake.f2, 1, 37) # marker D1M437
plot.pxg(fake.f2, mname)

mname2 <- find.marker(fake.f2, "X", 14) # marker DXM66
plot.pxg(fake.f2, mname2)

plot.pxg(fake.f2, c(mname,mname2))

[Package qtl version 0.99-24 Index]