qtl (version 0.97-21)

plot.pxg: Plot phenotypes versus marker genotypes.

Description

Plot the phenotype values versus the genotypes at a marker.

Usage

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

Arguments

x

An object of class cross. See read.cross for details.

marker

A marker name (a character string).

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.

...

Ignored at this point.

Value

• Returns a list with two components. The first component is a nominal p-value corresponding to a test of a difference between the genotype-specific phenotypic means. The second component is a matrix with three columns: the genotypes at the marker, the phenotypes, and a 0/1 indicator with 1's corresponding to inferred genotypes.

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 $\pm$ 1 SE.

See Also

find.marker, effectplot

Examples

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

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

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