effectscan {qtl}R Documentation

Plot allelic effect across the whole genome


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.


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,


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.




Hao Wu, hao@jax.org

See Also

effectplot, plot.pxg


# 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")

[Package qtl version 0.98-57 Index]