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, ...)

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.
... 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

Returns a list with six components.

Rsq R-square, or explained variation.
p.value Vector of p-values corresponding to an overall test of a difference between the genotype-specific phenotypic means, and marker main effects and interactions, if there is more than one marker. If there are multiple markers and some missing genotypes, interactions are collapsed into one component labeled inter.
me Means by marker.
se Standard errors by marker.
fit The aov fit.
data Matrix with at least three columns: the genotypes at each marker, the phenotypes, and a 0/1 indicator with 1's corresponding to inferred genotypes.

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 0.98-57 Index]