plot.pxg {qtl} | R Documentation |
Plot the phenotype values versus the genotypes at a marker.
plot.pxg(x, marker, pheno.col=1, jitter=1, infer=TRUE, ...)
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. |
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.
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.
Karl W Broman, kbroman@jhsph.edu
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)