qtl (version 1.01-9)

plot.errorlod: Plot grid of error LOD values

Description

Plot a grid of the LOD scores indicating which genotypes are likely to be in error.

Usage

plot.errorlod(x, chr, ind, breaks=c(-1,2,3,4.5,Inf),
              col=c("white","gray85","hotpink","purple3"), ...)

Arguments

x

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

chr

The chromosomes for which the error LOD scores should be plotted.

ind

Indicates the individuals for which the error LOD scores should be plotted.

breaks

A set of breakpoints for the colors; must give one more breakpoint than color. Intervals are open on the left and closed on the right, except for the lowest interval.

col

A vector of colors to appear in the image.

...

Ignored at this point.

Value

• None.

Details

Uses image to plot a grid with different shades of pixels to indicate which genotypes are likely to be in error.

Darker pixels have higher error LOD scores: $LOD \le 2$ in white; $2 < LOD \le 3$ in gray; $3 < LOD \le 4.5$ in pink; $LOD > 4.5$ in purple.

References

Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604--610.

See Also

calc.errorlod, top.errorlod, image

Examples

data(hyper)
hyper <- subset(hyper,chr=c(1,19))
# 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