plot.mpqtl: Plot output from interval mapping with detected QTL

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Plot -log10(p-value) or test statistic against cM position for (composite) interval mapping in multi-parent crosses. QTL support intervals are indicated with rectangles surrounding peaks.

Usage

## S3 method for class 'mpqtl'
plot(x, wald = FALSE, chr, lodsupport = 1, ...)

Arguments

x	Object of class mpqtl
wald	Flag for whether to plot the Wald statistic or -log10(p)
chr	Set of chromosomes to plot
lodsupport	x-LOD support interval plotted in green
...	Additional arguments to plotting function

Value

Plots the -log10(p) or Wald statistic for all chromosomes against the total genome in cM. QTL support intervals are indicated with shaded rectangles surrounding peaks

See Also

mpIM, summary.mpqtl

Examples

sim.map <- qtl::sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, 
	qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), 
		nrow=2, ncol=6, byrow=TRUE), seed=1)
mpp.dat <- mpprob(sim.dat, program="qtl", step=2)
mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
plot(mpq.dat)

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.