qtl (version 1.01-9)

effectscan: Plot allelic effect across the whole genome

Description

This function is used to plot allelic effect at all markers for selected chromosomes. For backcross, there will be only one line represents the additive effect. For F2, there will be two lines represent additive and dominance effects.

Usage

effectscan(cross, pheno.col=1, chr, ylim, gap=25,
           col=c("black","blue","red"), lty=c(1,2,3), lwd=2,
           mtick=c("line", "triangle"), main, add.legend=TRUE,
           ...)

Arguments

cross

An object of class cross.

pheno.col

Column number in the phenotype matrix which to be drawn in the plot.

chr

Chromosome number to be drawn in the plot.

ylim

y-axis limit.

gap

Gap separating chromosomes (in cM).

col

Line colors.

lty

Line types.

lwd

Line widths.

mtick

Tick mark type for markers.

main

Figure title.

add.legend

A logical value to indicate add legend or not.

...

Passed to the function plot when it is called.

Value

• None.

See Also

effectplot, plot.pxg

Examples

data(fake.f2)
# allelic effect on whole genome
effectscan(fake.f2, ylim=c(-6,3))
# on first 4 chromosomes, use triangle as marker ticks
effectscan(fake.f2, chr=1:4, ylim=c(-6,3), mtick="triangle")