qtl (version 0.92-3)

plot.geno: Plot observed genotypes, flagging likely errors

Description

Plot the genotypes on a particular chromosome for a set of individuals, flagging likely errors.

Usage

plot.geno(x, chr, ind, horizontal=FALSE, cutoff=2,
          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

Genotypes with error LOD scores above this value are flagged as possible 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

• None.

Details

Plots 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.

See Also

calc.errorlod, plot.errorlod, top.errorlod, image

Examples

data(hyper)
# run calc.genoprob, then calc.errorlod; use same error.prob
hyper <- calc.genoprob(hyper,error.prob=0.01)
hyper <- calc.errorlod(hyper,error.prob=0.01)

# plot the error LOD scores; print those above a specified cutoff 
plot.errorlod(hyper)
plot.errorlod(hyper,chr=1)
top.errorlod(hyper,cutoff=4)

# plot genotype data, flagging genotypes with error LOD > cutoff
plot.geno(hyper, chr=1, ind=160:200, cutoff=7, min.sep=2)

# Note that if markers are extremely tightly linked,
#     any recombination event will have a high error LOD
plot.geno(hyper, chr=1, ind=101:118, min.sep=2)
hyper$geno[[1]]$map