plot.geno {qtl}R Documentation

Plot genotypes with indication of likely errors

Description

Plot genotypes on a particular chromosome for a set of individuals, with an indication of likely errors.

Usage

plot.geno(x, chr, ind, horizontal=FALSE, cutoff=2,
         method=c("lod","argmax"), min.sep=1,...)

Arguments

x An object of class cross. See read.cross for details.
chr Chromosome number to plot.
ind Vector of individuals to plot. If missing, all individuals are plotted.
horizontal If TRUE, chromosomes are plotted horizontally.
cutoff Cutoff on error LOD score (if that method is used); genotypes with error LOD scores above this cutoff are flagged as errors.
method Indicates whether to use the error LOD scores calculated by calc.errorlod or the results of argmax.geno and find.errors.
min.sep Markers separated by less than this value (as a percent of the chromosome length) are pulled apart, so that they may be distinguished in the picture.
... Ignored at this point.

Value

A plot of the genotypes for a set of individuals. Likely errors are indicated by red squares. In a backcross, genotypes AA and AB are indicated by white and black circles, respectively. In an intercross, genotypes AA, AB and BB are indicated by white, gray, and black circles, respectively, and the partially missing genotypes "not BB" (D in mapmaker) and "not AA" (C in mapmaker) are indicated by green and orange circles, respectively.

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

See Also

image, plot.cross

Examples

data(listeria)
listeria <- calc.genoprob(listeria,error.prob=0.01)
listeria <- calc.errorlod(listeria,error.prob=0.01)
plot.geno(listeria,13)
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